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Name Description Links
a package (consisting of a suite of five programs: 2dx_manager, 2dx_image, 2dx_diffraction, 2dx_merger and 2dx_logbrowser) for user-friendly image processing of 2D crystals.
a tool for quantifying directional resolution and density isotropy of cryoEM maps using a 3D Fourier Shell Correlation (FSC) algorithm.
a versatile, integrated software system for the analysis, rebuilding, and visualization of 3-dimensional nucleic acid structures.
a CTF Estimator. ACE2 is a completely rewritten version of ACE. ACE2 adds the additional feature of robust astigmatism estimation and CTF correction with astigmatism using either a mild Weiner filter (recommended) or phase-flipping. Since ACE2 is written in objective C, it no longer requires MATLAB to work.
a heavily optimized molecular dynamics (MD) engine specially designed to run on NVIDA GPUs. It is extremely fast (115ns/day for DHFR using 1 GPU) and performs MD simulations on the microsecond scale in a single workstation. ACEMD can read CHARMM/NAMD and AMBER input files, works with CUDA and OpenCL, and uses similar syntax to other MD software.

Restriction: available to nonprofit users who register using the htmd_register command.
a tool that displays protein crystallography X-ray diffraction data. The data may be displayed as a 2-D image, 3-D wire mesh or as integer pixel values. Data files may be saved in tiff or postscript format.
a tool for predicting and modeling protein complexes with deep learning.
a fast and easy-to-use program that allows optimal visualization of PILATUS and EIGER data, and ALBULA API, a Python programming interface for displaying images and performing operations and calculations. The API enables you to easily integrate the viewer functionality into your beamline infrastructure or experimental setup. Consists of the standalone program ALBULA VIEWER.
an interactive perl/tk application that can read common sequence alignment formats that the user can then alter, embellish, markup, etc. to produce the kind of sequence figure commonly found in biochemical articles.
a modified version of AlphaFold, fine-tuned with a flow matching objective, designed for generative modeling of protein conformational ensembles.
an implementation of the inference pipeline of AlphaFold using a completely new model that was entered in CASP14.
a multipurpose Python script for producing plots and user-legible files from the output of AlphaFold2 (notebook) and Colabfold (notebook).
a Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer.
a program to format multiple sequence alignments in PostScript for publication and to assist in analysis. Alscript does not support point-and-click, but has a scripting language to allow complex effects.
Keywords:
Other
a suite of biomolecular simulation programs. It began in the late 1970's, and is maintained by an active development community.
a suite of programs that allows users to carry out molecular dynamics simulations, particularly on biomolecules. The suite can be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB) with either explicit water or generalized Born solvent models. The independently developed packages work well by themselves, and with Amber itself.
a tool that allows the user to perform interactive comparisons between RNA structures and to conduct database searches for specific RNA structures or substructures.
a best-in-class protein Language Model (pLM) that is orders of magnitude less expensive to train and deploy than previous models.
(Alignment of Multiple Protein Sequences) a suite of programs for protein multiple sequence alignment, pairwise alignment, statistical analysis and flexible pattern matching.
an open-source, community-driven analysis and visualization platform for ‘omics data. Its interactive interface facilitates the management of metagenomic contigs and associated data for automatic or human-guided identification of genome bins and their curation.
(Adaptive Poisson-Boltzmann Solver) a software package designed for the numerical solution of the Poisson-Boltzmann equation (PBE), solves the equations of continuum electrostatics for large biomolecular assemblages.
a suite of programs that analyze the quality of biomolecular structures determined via NMR spectroscopy. AQUA was initially developed by Ton Rullmann and Jurgen Doreleijers at the Bijvoet Center for Biomolecular Research, Utrecht,
a structure-solution program that constitutes a general crystallographic Ab Initio macromolecular phasing method for 2Å data, based on the combination of location of model fragments like small α-helices with PHASER and density modification with SHELXE.
AR-Decon, which stands for correcting Anisotropic Resolution by Deconvolution, is a computational pipeline designed to enhance the quality of three-dimensional maps that suffer from anisotropic resolutions, often resulting from datasets with preferred orientations. By applying advanced deconvolution techniques, AR-Decon corrects these resolution discrepancies, leading to more accurate and isotropic 3D maps.
(Alignment and Reconstruction for Electron Tomography) is a GPU-accelerated software package that provides an integrated solution to both fiducial-free alignment and reconstruction for cryoEM tomography.
(Alignment and Reconstruction for Electron Tomography 2) is a GPU-accelerated software package that provides an integrated solution to both fiducial-free alignment and reconstruction for cryoEM tomography.
a multi-GPU accelerated software package that enables real-time fully automated reconstruction of cryoET tomograms in parallel with cryoET data collection.
(Ambiguous Restraints for Iterative Assignment) a software that automates NOE assignment and NMR structure calculation.
Keywords:
NMR
a lightweight multi-protocol & multi-source command-line download utility. It supports HTTP/HTTPS, FTP, SFTP, BitTorrent and Metalink. aria2 can be manipulated via built-in JSON-RPC and XML-RPC interfaces.
Keywords:
Other
an interpretation of crystallographic electron density maps and automatic construction and refinement of macromolecular models.

Restriction: available to nonprofit users who register and download ARP/wARP individually. See detailed instructions.
a Java application that allows you to design your RNA 2D structure interactively and to create and assemble the corresponding RNA 3D modules directly in UCSF Chimera.
an assembly line of macromolecular assemblies, Assembline is a multi-step protocol for integrative structural modeling of macromolecular complexes based on electron microscopy, cross-linking mass spectrometry and other data.
a program suite for small-angle scattering (SAXS) data analysis from biological macromolecules.

March 4, 2025 Version 4.0.1 uses new registration page: https://biosaxs.com/download Restriction: available to nonprofit users who register with EMBL & submit confirmation to SBGrid.

Keywords:
SAXS
Other
an automated image reconstruction system that coordinates the execution of the parallel, numerically-intensive codes P3DR, PCUT, POR, PPFT, PSF and RobEM (a GUI driven program used both for image preprocessing and visualization).
a suite of automated docking tools designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of a known 3D structure.
a Cuda accelerated version of AutoDock4.2.6, AutoDock for GPUs and other accelerators. It leverages its parallelizable LGA by processing ligand-receptor poses in parallel over multiple compute units. The Cuda version was developed in collaboration with Nvidia to run AutoDock-GPU on the Oak Ridge National Laboratory's (ORNL) Summit, and it included a batched ligand pipeline developed by Aaron Scheinberg from Jubilee Development.
a program for drug discovery, molecular docking, and virtual screening, offering multi-core capability, high performance and enhanced accuracy and ease of use.
an open-source program for semi-automated computer-aided drug discovery. It uses a genetic algorithm to evolve predicted ligands on demand and so is not limited to a virtual library of pre-enumerated compounds.
a tool that combines third-party processing programs with new tools for automated data processing of single-sweep, multi-sweep and multi-crystal X-ray diffraction data.

Restriction: available to non-profit users who register with Global Phasing and copy license file to /programs/local/autoproc/autoproc_licence.
an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.
(Amazon Web Services Command Line Interface) a command line interface tool to manage multiple Amazon Web Services and automate them through scripts.
Keywords:
Other
a system that aims to integrate into one system all the components necessary for finding a solution structure by MR. It consists of a database, scientific programs and a python pipeline. The system is automated and needs no user intervention when running a complicated combination of jobs, such as model searching, molecular replacement and refinement.
a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic. Bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), sophisticated analyses …
Keywords:
Other
a program for optimal planning of X-ray data collection from protein crystals.

Restriction: available to nonprofit users who register with EMBL & submit confirmation to SBGrid.
a program for filtering 3D maps and applying B-factors.
a program to convert images saved in FEI's bin format into MRC/CCP4 format.
a user friendly and accurate binder design pipeline.
a set of command line tools written in C and making use of the BiopLib library for manipulation of protein structure and sequence.
Keywords:
Other
a program for analysis of SAXS data that enables creation of 1D scattering profiles from 2D detector images, standard data operations such as averaging and subtraction, analysis of radius of gyration (Rg) and molecular weight, and advanced processing using GNOM, DAMMIF, and AMBIMETER. It also allows easy processing of inline SEC-SAXS data.
Keywords:
SAXS
Other
(Basic Local Alignment Search Tool) finds regions of similarity between biological sequences.
a suite of BLAST (Basic Local Alignment Search Tool) tools that utilizes the NCBI C++ Toolkit with a number of performance and feature improvements over the legacy BLAST applications.
a 3D creation suite that supports the entirety of the 3D pipeline—modeling, rigging, animation, simulation, rendering, compositing and motion tracking.
(Buffalo n' Pittsburgh Interface) a program that combines SnB and the Phases Suite; for complete protein phasing.
an extension to Molscript that adds sticks and spheres, stereo pictures, flexible colouring (colour ramping) and map drawing.
an open-source model which predicts the 3D structure of proteins, rna, dna and small molecules; it handles modified residues, covalent ligands and glycans, as well as condition the generation on pocket residues.
an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for microbial sized genomes. It reports single-nucleotide mutations, point insertions and deletions, large deletions, and new junctions supported by mosaic reads.
a collection of programs and a platform for the development of software for image processing of electron micrographs, interpretation of reconstructions, molecular modeling, and general image and molecular processing.
a suite of applications for the analysis of helical structures.
a software system containing crystallographic structure refinement using Bayesian statistical methods (BUSTER), ligand fitting (rhofit) and a fully automated pipeline (Pipedream) to drive a structure based fragment/ligand screening pathway.

Restriction: available to nonprofit users who register with Global Phasing and copy license file to /programs/local/buster/buster_licence.
(Computer Aided Resonance Assignment) an application for the analysis of NMR spectra and computer-aided resonance assignment.
Keywords:
NMR
a tool that merges crystallography data without much physics. It performs scaling, merging, and French-Wilson corrections in a single step by directly inferring structure factor amplitudes from unscaled, unmerged intensities.
a software tool for the analysis and visualisation of tunnels and channels in protein structures. This is the command line version, not the PyMOL plugin version.
a software tool for the calculation, analysis, and real-time visualization of access tunnels and channels in static and dynamic protein structures with an intuitive GUI.
a software for protein residue-residue Contacts from Correlated Mutations PREDicted quickly and accurately.
Keywords:
Other
(Collaborative Computational Project, Number 4) a collection of programs and associated data and software libraries used for macromolecular structure determination by X-ray crystallography.
a tool that offers a quick and easy way to create beautiful publication quality images and movies and to superpose and analyze structures.
(Collaborative Computational Project for Electron cryo-Microscopy) a software framework and resulting software suite that includes tools for project and data management along with a focus on building and refinement of atomic models into cryo-EM reconstructions. The framework allows easy access to various programs and utilities from collaborators via Python task wrappers and a user-friendly graphical user interface or a command-line interface suitable for scripting.
a series of programs for macromolecular NMR including AnalysisAssign, AnalysisScreen, AnalysisMetabolomics and AnalysisStructure, and with version 3, the addition CcpNmr ChemBuild.
Keywords:
NMR
a graphical tool to construct chemical compound definitions for NMR, created to handle concepts like protonation variants and magnetic equivalence that are required for NMR resonance assignment. Several different chemical file formats are supported, including PDB, .mol and .mol2, but ChemBuild is special in its ability read and write CCPN chemical component XML files, which store NMR-aware information.
Keywords:
NMR
a cell image analysis software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.
a multi-modal foundation model for molecular structure prediction that performs at the state-of-the-art across a variety of benchmarks. Chai-1 enables unified prediction of proteins, small molecules, DNA, RNA, glycosylations, and more.
(The Channel Annotation Package) a tool for the functional annotation of novel ion channel structures that provides information on the biophysical properties of the ion permeation pathway by utilising molecular dynamics simulations.
a sequence assignment validation tool for in cryo-EM models
a tool that utilizes information from Cryo-EM density and state-of-the-art small molecule force fields to dock small molecules into protein targets.
an analysis program for chemical exchange detected by NMR.
Keywords:
NMR
a highly extensible, interactive molecular graphics program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. It is often a tool of choice for rendering EM volumes.
a tool of the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. Compared to Chimera, ChimeraX has improved graphics (e.g. interactive ambient shadows); faster handling of large structures (millions of atoms); and a more modern, single-window user interface.
a generative model for designing proteins programmatically.
an automatic 2d class selection tool based on a deep learning network to separate 2D classes from .hdf / .mrcs files into good and bad classes. Cinderella uses the same deep neural network as crYOLO and was pretrained on a set good / bad classes.
(Computational Imaging System for Transmission Electron Microscopy) a program that processes cryo-EM images of macromolecular complexes and obtains high-resolution 3D reconstructions with tools to process image data including movies, micrographs and stacks of single-particle images, implementing a complete “pipeline” of processing steps to obtain high-resolution single-particle reconstructions.
a general purpose multiple sequence alignment program for DNA or proteins.
Keywords:
Other
a multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences.
Keywords:
Other
an interactive contact map visualization and analysis tool.
(Crystallography & NMR System) an X-ray crystallography suite used for refinement, phasing, and molecular replacement.
a tool that makes Run VS Code on any machine anywhere and access it in the browser.
a tool that makes protein design accessible through Jupyter notebooks by using advanced protein structure prediction models like AlphaFold and TrRosetta for designing novel proteins with targeted structures.
an easy-to-use Notebook based environment for fast and convenient protein structure predictions.
a pipeline that predicts the structure of large protein complexes starting from the sequences of chains in the complex, accommodating up to 18,000 amino acids and 32 subunits.
a program for molecular replacement calculations, using the combined molecular replacement method.
a tool that makes ligand binding site prediction from protein sequence and structure.
a method to generate protein conformations around a known structure based on geometric restrictions.
(Crystallographic Object-Oriented Toolkit) an application that supports model building and real space refinement. This application interfaces with refmac, Phenix, and several other applications. Coot was recognized as the best structural biology application in 2008 by SBGrid.
a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. CP2K provides a general framework for different modeling methods such as DFT using the mixed Gaussian and plane waves approaches GPW and GAPW. Supported theory levels include DFTB, LDA, GGA, MP2, RPA, semi-empirical methods, and classical force fields.
a program for non-linear least squares fitting of CPMG relaxation dispersion curves.
Keywords:
NMR
a tool that enables the easy detection of CRISPRs and cas genes in user-submitted sequence data (allows sequences up to 50 Mo otherwise download standalone program). This is an update of the CRISPRFinder program with improved specificity and indication on the CRISPR orientation. MacSyFinder is used to identify cas genes, the CRISPR-Cas type and subtype.
a program for cutting sections out of 2D and 3D density maps.
a merged hkl-file into k subsets with the number of reflections marked with -1; crossflaghkl partitions.
a software that automatically constructs full-atom 3D structural models of proteins based on cryo-EM density maps and sequence information.
an automatic pipeline for cryo-EM data preprocessing and assessment using a combination of deep learning and image analysis tools.
a restoration method that dramatically increases contrast in cryo-TEM images, improving the interpretability of the acquired data. PIP package memory efficient implementation of cryoCARE (Content-Aware Image Restoration for Cryo-Transmission Electron Microscopy Data).
a neural network based algorithm for heterogeneous cryo-EM reconstruction. In particular, the method models a continuous distribution over 3D structures by using a neural network based representation for the volume.
an open-source software package for robust analysis of the orientation distribution of cryoelectron microscopy data.
a graphical user interface for identification of proteins from cryo-EM maps.
a novel automated particle picking software based on the deep learning object detection system 'You Only Look Once' (YOLO). CrYOLO is available as a standalone program under http://sphire.mpg.de/ and is part of the image processing workflow in SPHIRE.
a computational tool using deep learning to automatically build full DNA/RNA atomic structure from cryo-EM map.
a deep learning based tool for denoising cryo-ET datasets. It is designed to accept .mrc, .rc and .tif single 3D files, or can accept a sequence of 2D.tf files if a path is provided.
a tool for accurate cryo-EM protein particle picking by integrating the foundational AI image segmentation model and specialized U-Net
an advanced software solution designed for particle sorting/sieving in single particle analysis (SPA) for Cryogenic Electron Microscopy (cryo-EM).
a toolkit for interfacing with CryoSPARC.
a neural network based framework for recovering conformational heterogenity of protein complexes.
a suite of programs for processing diffraction data acquired "serially" in a "snapshot" manner, such as when using the technique of Serial Femtosecond Crystallography (SFX) with a free-electron laser source.
a simple utility that wraps around csparc2star.py to convert particle positions from Cryosparc JOB directories into a RELION-ready directory.
(Chemical-Shift-ROSETTA) a robust protocol to exploit mining of protein chemical shifts deposited in the BMRB, in conjunction with the known corresponding 3D structures for de novo protein structure generation, using as input parameters the 13CA, 13CB, 13C', 15N, 1HA and 1HN NMR chemical shifts. Also includes CS-Rosetta toolbox, which provides useful scripts for preparing, running, and analyzing CS-Rosetta runs.
Keywords:
NMR
a group of programs for finding CTFs of electron micrographs; CTFFIND3 and CTFTILT.
a new version of ctffind (a program for finding CTFs of electron micrographs) that should run significantly faster than CTFFIND 3 and may give slightly improved results when processing data from detectors other than scanned photographic film.
a new version of the cisTEM program CTFFIND with improved CTF estimation for cryoEM.
a tool that helps redistributable software libraries to support CUDA applications for Linux.
Keywords:
Other
an algorithm for calculating a helical parameter description for any irregular nucleic acid segment with respect to an optimal, global helical axis.
a complete rewrite of the Curves approach for analyzing the structure of nucleic acids. Included are the helper programs Canal, Cdif and Sumr.
a computational tool using deep learning that can estimate the residue-wise local quality for protein models from cryo-Electron Microscopy (EM) maps.
an Open-Source Program for Data Visualization and Analysis with Chemical Intelligence
a high quality open-source toolchain that democratizes the use of deep-learning in drug discovery, materials science, quantum chemistry, and biology.
a tool used for the implementation of a deep learning method for simultaneous denoising and missing wedge reconstruction in cryogenic electron tomography
(Deep cryo-EM Map Enhancer) a python package designed to perform non-linear post-processing of cryo-EM maps for local sharpening, automatic masking and denoising. Systems using cuda 11+ should use the 20210511 version of deepEMhancer, and the modified models distributed in /programs/share/deepemhancer/20210511/deepEMhancerModels/production_checkpoints/
a deep learning based open-source software with a friendly user interface to pick 3D particles rapidly and accurately from cryo-electron tomograms.
an original deep learning approach to localize macromolecules in cryo electron tomography images. The method is based on image segmentation using a 3D convolutional neural network.
Keywords:
Visualization
a deep-learning based method for de novo RNA tertiary structure prediction.
Deep functional residue identification
a de novo modeling protocol to build an entire protein 3D model directly from near-atomic (up to about 5 Angstrom) resolution EM map.
a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq.
(Dynamics Extraction From cryo-em Map); an implementation of a dynamics prediction from a cryo-EM density map.
a program for calculating protein electrostatics.

Restriction: available to nonprofit users who register with Columbia & submit confirmation to SBGrid.
a scoring function for rescoring protein-ligand binding affinity
a machine-learning based protein-ligand scoring function.
(DENsity from Solution Scattering) an algorithm used for calculating ab initio electron density maps directly from solution scattering data.
Keywords:
SAXS
Other
(Diffraction Integration for Advanced Light Sources) a software project for the analysis of crystallographic diffraction images for many new methods from shutterless, fine-sliced rotation scans to randomly-oriented snapshots of serial crystallography. It uses multiple CPU and GPU machines to increase speed and accuracy based on a comprehensive physical model.
a state-of-the-art method for molecular docking
a program to calculate difference maps between two density maps. The maps must have the same overall dimensions and need to be aligned with each other.
a realtime 3D visualization program for structural biology data.
a tool that performs efficient geometry-based conformational sampling of protein structures under experimental restraints. It combines prior structural information with experimental data through the Deformable Elastic Network (DEN) approach which drastically reduces over-fitting.
a molecular docking application used to a) predict binding modes of small molecule-protein complexes; b) search databases of ligands for compounds that inhibit enzyme activity, bind a particular protein, bind nucleic acid targets; c) examine possible binding orientations of protein-protein and protein-DNA complexes; d) help guide synthetic efforts by examining small molecules that are computationally derivatized. Dock is offered in the SBGrid collection in …
a program that sorts particles by size using the radius of a particle; it uses difference of Gaussians (DoG) for picking particles.
a tool designed for de novo identification of protein domains in cryo-ET maps of protein complexes.
a new web-based user interface for CCP-EM and RELION software.
a tool for nucleic acid sequence identification, assignment and validation for cryo-EM and crystal structure models.
a program that surveys a protein molecule's structure to locate internal cavities and assess hydrophilicity in terms of the energy of interaction of a water molecule with the surrounding atoms. Experience has shown that cavities with interaction energies below -12 kcal/mol tend to be filled, and cavities for which the energy is above that threshold, tend to be empty.
(Data Processing Suite) a suite of programs for processing single crystal X-ray diffraction data of proteins, viruses, nucleic acids and other large biological complexes, with an emphasis on data collected at synchrotron sources.
a neural network-based algorithm for ab initio heterogeneous cryo-EM reconstruction.
a program that standardizes secondary structure assignment calculated from a coordinate file. Secondary structure prediction is not supported. Designed by Wolfgang Kabsch and Chris Sander
(Dissecting the Spatial Structure of RNA) a software tool for dissecting the spatial structure of RNA.
a software suite and toolkit that processes single crystal X-ray diffraction images from two-dimensional position sensitive detectors.

Restriction: available to users with an activate d*TREK software license.
a software suite and toolkit that processes single crystal X-ray diffraction images from two-dimensional position sensitive detectors. This entry is for the free version of d*TREK.
(Dials User Interface) a GUI to allow the general user to run DIALS tools and inspect the output without resorting to detailed command-line usage.
a XDS plugin for reading HDF5 files following the NeXuS format or those written by Dectris Eiger detectors.
a software environment for subtomogram averaging of cryo-EM data.
a small set of tools providing a bidirectional interface between the subtomogram averaging software Dynamo and the Warp-RELION-M pipeline.
a tiny function to convert Dynamo tables to star files for RELION 4.0
a collection of tools for subtomogram averaging in dynamo.
a program to determine domains, hinge axes and hinge bending residues in proteins where two conformations are available.
a program to analyze domain movements in large, multi-chain, biomolecular complexes, useful for any molecule for which two atomic structures are available that represent a conformational change indicating a possible domain movement.
a Bioconductor software package installed in R 3.2.2 for gene and isoform differential expression analysis of RNA-seq data.
a crystallographic real-space electron-density refinement and optimization program that produces electron density maps with minimal model bias in a robust manner.
a simple program that converts diffraction images from EIGER in the HDF5 format to the miniCBF format.
(ELECtron Tomography Resolution Assessment) a suite of programs written to estimate the resolution of electron density volumes obtained by electron tomography.
a tool that automates most of the repetitive and mindless procedures used in solving macromolecular crystal structures, and is capable of autonomously carrying out all the steps needed to convert raw X-ray diffraction image data to a phased electron density map.
a program to convert images from/to formats used in the "electron microscopical community" (3DEM)
a suite of scientific image processing tools with a particular focus on single particle reconstruction and which includes Foldhunter and Helixhunter.
a scientific image processing suite with a particular focus on single particle reconstruction from cryoEM images. EMAN2 is a complete refactoring of the original EMAN1 library and contains the SPARX applications.
a computational tool using deep learning that can accurately identify structures, alpha helices, beta sheets, other(coils/turns) and DNA/RNA, in cryo-EM maps of medium to low resolution.
a program that allows sharpening of high resolution information in 3D maps obtained by electron cryomicroscopy according to the Rosenthal and Henderson approach (JMB 333:721-745, 2003).
a program that integrates a range of currently available packages and tools for sequence analysis into a seamless whole.
an automatic model building method of multi-chain protein complexes from intermediate-resolution cryo-EM maps, integrating AlphaFold structure prediction, FFT-based global fitting, domain-based semi-flexible refinement, and graph-based iterative assembling on the main-chain probability map predicted by a deep convolutional network.
(enhanced macromolecular classification and alignment for high-resolution in situ tomography) a GPU-accelerated image processing software for high-resolution cryo-electron tomography and subtomogram averaging and classification.
a computational tool which enables capturing protein structure information from cryo-EM maps more effectively than raw maps.
(EM Imaging Processing GUI) a Graphical User Interface that collects information from the user and runs existing programs from a variety of different software packages.
a tool that improves the quality and interpretability of cryo-EM maps by local and non-local deep learning
a deep learning based automated RNA modeling from cryo-EM maps.
a JAVA program that reads PDB files containing a nucleic-acid protein complex and gives a listing of interactions that occur at the interface between the nucleic-acid/protein complex and classifies these interactions into hydrogen bonds, electrostatic, hydrophobic, and Van der Waals. Entangle also recognizes when a stacking interaction occurs between two aromatic residues.
a program that finds crystallographic molecular replacement solutions using an evolutionary search algorithm. The program directly optimizes three rotational and three positional parameters for the search model with respect to the correlation coefficient between Fo and Fc.
(retired)
a script driven program that analyzes and compares three-dimensional protein structures. The current version (0.7) is mostly designed to find the rigid part of protein molecules by comparing different structures.

Restriction: available to nonprofit users who register with EMBL & submit confirmation to SBGrid.
a program that harnesses the ESM-2 language model to generate accurate structure predictions end to end directly from the sequence of a protein.
(Easy Sequencing in Postscript) a utility to generate a pretty PostScript output from aligned sequences and coordinate files.
Keywords:
Other
a tool that performs RNA secondary structure prediction.
a tool to predict protein structure, function, and mutations using evolutionary sequence covariation.
a program for DNA foundation modeling from molecular to genome scale
a DNA and protein sequence alignment software package that searches for matching sequence patterns or words, called k-tuples.
a Perl program to assist in the analysis of laboratory frame spin relaxation data. It interfaces with ModelFree 4.01 (A. G. Palmer, Columbia University) and fully automates the process of model selection and tensor optimization.
Keywords:
NMR
an application for Efficient Data Transfers which is capable of reading and writing at disk speed over wide area networks (with standard TCP). It is written in Java, runs an all major platforms and it is easy to use.
Keywords:
Other
a Python package for detecting and erasing gold fiducials in cryo-EM images.
an image processing package. It can be described as a distribution of ImageJ (and ImageJ2) together with Java, Java 3D and a lot of plugins organized into a coherent menu structure. Fiji compares to ImageJ as Ubuntu compares to Linux.
Keywords:
Other
a popular way to view DNA sequence traces on Linux, Mac OSX, Windows, and Solaris. FinchTV started as the only chromatogram viewer that can display an entire trace in a scalable multi-pane view. And it leads the way with raw data views, BLAST searching and the ability to reverse complement sequences and traces.
Keywords:
Other
a tool that determines the detective quantum efficiency (DQE) of a detector.
an interface for cryo-transmission electron microscopy (cryo-EM) data collection with computer image processing. Focus creates a user-friendly environment to import and manage data recorded by direct electron detectors and perform elemental image processing tasks in a high-throughput manner, while new data is being acquired at the microscope.
a program that enables fast and sensitive comparisons of large structure sets.
a snakemake workflow for making and benchmarking structure based trees using Foldseek.
a program for tomogram binning in Fourier space.
an open source protein pocket (cavity) detection algorithm based on Voronoi tessellation. It was developed in the C programming language and is currently available as command line driven program.
a simple package for fast molecular similarity searches
a program that merges, links, and places compounds by stitching bound compounds together like a reanimated corpse.
(Fourier REconstruction and ALIGNment) a program for high-resolution refinement of 3D reconstructions from cryo-EM images of single particles.
a program for the refinement of helical filament reconstructions from cryo electron micrographs. It is primarily used to process images of amyloid fibrils, though it has also been tested on TMV and actin filaments.
a C library and C++ command line tool for calculating Solvent Accessible Surface Area (SASA) of biomolecules.
(Fast Rotational DOCKing) a tool used to efficiently generate many potential predictions of how two proteins could interact.
(Function and Data Analysis) a program whose nmrPipeFit component is designed to analyse nD (n>1) NMR correlation spectra. The program is currently designed for arrayed 2D spectra, such as relaxation experiments and diffusion experiments, and simple 2D and 3D spectra.
Keywords:
NMR
(General Approach to Magnetic resonance Mathematical Analysis) a package of C++ libraries that allow simulation of magnetic resonance (NMR, MRS) experiments. It is used for designing and analyzing NMR pulse sequences.
Keywords:
NMR
is GPU-Accelerated Python STOPgap for Template Matching for fast template matching (TM) in cryo electron tomograms that is based on TM routines from STOPGAP.
a GPU-accelerated program for accurate, fast, flexible and fully automatic particle picking from cryo-EM micrographs with or without templates.
a set of tools and libraries for interacting with Google Cloud products and services.
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Other
a GPU accelerated program for accurate and robust, real-time CTF determination of EM Micrographs.
a tool that robustly estimates the contrast transfer function (CTF) of cryoET tilt series and cryoEM micrographs, essential information needed for cryoET subtomogram averaging and cryoEM single-particle reconstruction.
a version of FREALIGN modified to run on GPU processors so that the refinement process of single particle 3D reconstruction can be speedup.
a powerful and comprehensive suite of molecular biology and NGS analysis tools.

Restriction: shared license available to non-profit groups as add-on option.
a GPU-enhanced version of RELION that dramatically speeds up 2D/3D classification and 3D auto-refine.
an interpreter for the PostScript (TM) language. It can display and convert postscript files. Software can be involved with gs command.
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Other
a GPU accelerated program, can translationally and rotationally localize the target protein complex in cellular lamellae, as prepared with a focused ion beam, using single cryo-electron microscopy images without tilt-series, and reconstruct the protein complex at near-atomic resolution.
a program that combines installation of autoPROC, BUSTER, and SHARP available to Global Phasing consortium members.

Restriction: available to Global Phasing Consortium members with an active license.
(Globus Command Line Interface) a command line wrapper over the Globus SDK for Python. It is a standalone application that can be installed on the user’s machine and used to access the Globus service.
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Other
a versatile markdown tool offering both a text-based user interface (TUI) for interactive browsing and a command-line interface (CLI) for direct manipulation of markdown content.
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Other
a tool that superimposes molecular subunits into the density map of their complex. To reduce computational costs for the superimposing, both subunits and complexes are transformed into GMM (Gaussian Mixture Model) using the gmconvert program. Although designed to superimpose multiple atomic models of subunits into a low-resolution 3D density map, gmfit can also be applied to superimposing two 3D density maps or two atomic …
a portable command-line driven graphing utility originally created to allow scientists and students to visualize mathematical functions and data interactively. It has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by third-party applications like CCP4 and Octave.
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Other
(geometrically optimized CTF determination for single-particle cryo-EM) a program explicitly designed to determine the focus gradient in single-particle cryo-EM using a novel geometrically optimized approach. The goCTF software is built on the open-source code of CTFFIND4.
an interactive molecular modeling system specifically geared towards cryo-EM and other low resolution structures of macromolecular complexes. The long term goal of the gorgon project is to be able to address to every part of the molecular modeling pipeline starting from the initial volumetric reconstruction of the complex all the way to the final placement of each individual atom.
a general plotting, curve fitting and data transformation program.
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Other
an open-source graph visualization software program. A gallery of images is available on the developer's website: http://www.graphviz.org/Gallery.php
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Other
a versatile package that performs molecular dynamics of proteins, lipids and nucleic acids.
a novel high-performance protein structure alignment, superposition and search method with flexible structure clustering ability.
a program based on the implementation of AutoDock Vina, GWOVina employs grey wolf optimization (GWO) algorithm to speed up the search for optimal ligand poses.
a modular program for SPM (scanning probe microscopy) data visualization and analysis.
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Other
a tool used by the XDS package for the processing of EIGER HDF5 data.
(High Ambiguity Driven biomolecular DOCKing) relies on an approach that makes use of biochemical and/or biophysical interaction data, such as chemical shift perturbation data resulting from NMR titration experiments, mutagenesis data or bioinformatic predictions.
a neural network for the automatic identification of oligonucleotides and protein secondary structure in cryo‐EM maps.
a program suite (hbplus, access and clean) to compute hydrogen positions, hydrogen bonds, and neighboring interactions. The application was developed at University College London.
an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).
a data processing suite for X-ray crystallography that provides a sleek interface for devising a data collection strategy and processing data. HKL is based on the extended versions of Denzo, Xdisplayf and Scalepack. HKL was developed and is maintained by Wladek Minor (University of Virginia).

Restriction: must obtain software license from developer & copy license file to /usr/local/lib.
a graphical user-interface for macromolecular phasing.

Available to nonprofit users who register with EMBL & submit confirmation to SBGrid.
a program that allows the analysis and visualisation of the pore dimensions of the holes through molecular structures of ion channels.
(Hypergeometric Optimization of Motif EnRichment) a suite of sequencing analysis and sequence motif discovery tools.
a high performance soft fork of OpenSSH that can provide significnatly faster throughput for bulk data transfers over a wide range of network paths.
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Other
a program intended for the calculation of NMR relaxation of small, quasirigid macromolecules whose structure, with atomic resolution, is taken from a PDB file of atomic coordinates. HYDRONMR evaluates basic hydrodynamic quantities involved in dynamic NMR in the same fashion as HYDROPRO program, then calculates NMR quantities (T1, T2, NOE, etc) for each residue of a globular protein and reports the translational diffusion coefficient, …
Keywords:
NMR
a program that computes the hydrodynamic properties of rigid macromolecules (proteins, small nucleic acids, macromolecular complexes, etc.) from their structure, as specified by the coordinates taken from a PDB file supplied by the user, from which the proper hydrodynamic model is built by the program itself.
a software for ice gradient estimation and removal on cryoEM micrographs.
a high quality visualizer and annotator for three dimensional molecular structures, sequences, alignments, chemical spreadsheets and biological data.
(Intrinsically Disordered Proteins Conformer Generator) a flexible, modular platform for generating ensembles of disordered protein states that builds conformers by sampling backbone torsion angles of relevant sequence fragments extracted from protein structures in the RCSB Protein Data Bank.
Keywords:
NMR
(Integrative Genomics Viewer) a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.
a user-friendly extension to Ed Egelman's Iterative Helical Real Space Reconstruction (IHRSR) software that includes the original IHRSR functionality but can also determine out-of-plane tilt, apply dihedral symmetry, and automatically construct a starting model from the image data Perl and Spider scripts allow users to perform common tasks: power spectra calculations, CTF corrections, image stack generation, image centering, and tube diameter determination.
a simple, user-friendly tool for interactive image classification, segmentation and analysis. It is built as a modular software framework, which currently has workflows for automated (supervised) pixel- and object-level classification, automated and semi-automated object tracking, semi-automated segmentation and object counting without detection.
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Other
a small Fortran program for creating non-photorealistic illustrations of molecules, with cartoony colors and outlines, and soft ambient shadows. I originally developed it during postdoctoral training in the laboratory of Arthur J. Olson at the Scripps Research Institute, and have tinkered with it ever since. I have used it to create materials for my books and for PDB-101, the outreach portal of the RCSB …
a Java image processing program inspired by NIH Image that can display, edit, analyze, process, save and print 8-bit, 16-bit, and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw" and supports "stacks", a series of images that share a single window. It is multithreaded, so time-consuming operations can be performed in parallel with other operations.
a software suite to create, edit, compose, or convert bitmap images.
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Other
a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections.
a tool reading IMOD points, obtaining particles' info and generating .star file for RELION.
an efficient tool for flexible fitting of atomic structures into EM maps based on Normal Mode Analysis in internal Coordinates.
a toolkit to perform Normal Mode Analysis (NMA) in internal coordinates (IC) on both protein and nucleic acid atomic structures. Vibrational analysis, motion animations, morphing trajectories and Monte-Carlo simulations can be easily carried out at different scales of resolution using this toolkit.
a data processing application for macromolecular crystallography. iMosflm (Graphical User Interface) and Mosflm (data processing application) are distributed with this package.
(Integrative Modeling Platform) a program designed to allow mixing and matching of existing modeling components as well as the easy addition of new functionality.
(INFERence of RNA ALignment) a program that searches DNA sequence databases for RNA structure and sequence similarities and uses a special case of profile stochastic context-free grammars called covariance models (CMs). In many cases It is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence.
a program for ab initio phase determination.
(Image Processing Library & Toolbox) a 2D Crystallography Suite developed by Andreas Schenk.
an immersive environment designed to ease the task of building high quality macromolecular models into low to medium resolution experimental maps, where the experimental information alone is insufficient to place individual atoms precisely. ISOLDE is implemented as a plugin to ChimeraX and can be conveniently installed via its built-in Tool Shed.
(ISOtropic reconstructioN of Electron Tomography) a tool that trains deep convolutional neural networks to reconstruct meaningful contents in the missing wedge for electron tomography, and to increase signal-to-noise ratio, using the information learned from the original tomogram.
an algorithm to reconstruct non-uniformly acquired NMR data.
Keywords:
NMR
a multiple sequence alignment editor written in Java. It is used widely in a variety of web pages (e.g. the EBI Clustalw server and the Pfam protein domain database) but is available as a general purpose alignment editor.
a lightweight and flexible command-line JSON processor.
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Other
a flexible dynamic language appropriate for scientific and numerical computing with performance comparable to traditional statically-typed languages.
a language-agnostic HTML notebook application for Project Jupyter.
a program for the next-generation web-based user interface for Project Jupyter. JupyterLab enables you to work with documents and activities such as Jupyter notebooks, text editors, terminals, and custom components in a flexible, integrated, and extensible manner.
(Karhunen Loeve Transform picker) a fully automatic EM particle picker and requires only the approximated particle size as an input . It is especially designed to handle low SNR micrographs. It is based on learning a set of optimal templates through the use of multi-variate statistical analysis via the Karhunen Loeve Transform.
a tool that finds the positions of phosphates and bases in electron density maps with a fairly high degree of reliability.
(Local-correlation-coefficient-based Automatic FItting for REfinement) an automatic refinement system for protein crystallography. The system starts with an initial model (approximate or partial model) and finishes with the final structure including water molecules. LAFIRE uses the refinement programs CNS or Refmac5.
a protein-protein, protein-peptide and protein-DNA docking framework based on the Glowworm Swarm Optimization (GSO) algorithm.
a program for automatically plotting protein-ligand interactions.
a successor to the original LIGPLOT program for automatic generation of 2D ligand-protein interaction diagrams. It is run from an intuitive java interface which allows on-screen editing of the plots via mouse click-and-drag operations.
a pipeline for simulation assisted interpretation of lipid or lipid-like densities in e.g. cryogenic electron microscopy (cryo-EM) structures of membrane proteins.
a tool that uses rotationally averaged reference amplitudes from a refined atomic model to locally scale (sharpen) amplitudes of the Fourier transform of a cryo-EM potential map, keeping the phases constant.
a novel deep learning framework that incorporates protein amino acid sequence and structural information to predict protein function.
a program for calculating the curvature of nucleic acids. From a given list of base pair step roll, tilt and twist values, and the specification of a reference plane, the program produces the global tilt, global roll and the bend magnitude. These quantities describe the direction and magnitude of a bend angle for analysis of DNA and DNA/protein complex geometries.
a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <200 sequences), FFT-NS-2 (fast; for alignment of <30,000 sequences).
a program used to estimate magnification distortions in electron micrographs using images of polycrystalline samples such as gold shadowed diffraction gratings. The measured distortion at a particular magnification can then be corrected in images of the sample using mag_distortion_correct. Both programs read images that are stored in MRC/CCP4 format.
a model building application for X-ray crystallography.
a package that does multiple alignment of protein structures, providing a common 3D superimposition, a corresponding structure-based sequence alignment and a dendrogram for the set of structures aligned.
a tool for assessing how well atomic model features are resolved in cryoEM maps. A fitted model is used in the analysis. A Q-score is calculated for each atom in the model. Q-scores can then be used to visualize how well each residue/atom is resolved and averaged to represent the entire model/map.
a python package for aligning and subtracting non-isomorphous crystallographic datasets.
a multiple protein structure alignment program. It uses local geometry to align segments of two sets of proteins, allowing limited bends in the backbones between the segments.
is a tool for the systematic analysis of compositionally-heterogeneous cryo-EM datasets. MAVEn is designed to work downstream of cryoDRGN, after users have generated a large number of maps (usually 500-1000) systematically sampling the latent space, but can be applied to any ensemble of volumes.
an application that assists in the processing and curation of macromolecular structure data.
(Multi-Conformation Continuum Electrostatics) a biophysics simulation program combining continuum electrostatics and molecular mechanics. In this program, the protein side chain motions are simulated explicitly while the dielectric effect of solvent and bulk protein material is modeled by continuum electrostatics.
a tool for mean curvature motion and levelset motion for cryo-ET
an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. It can write most of these formats, too, together with atom selections suitable for visualization or native analysis tools.
is a simple app to fetch acquisition metadata from a EPU session or SerialEM. It parses the first found xml/mdoc/mrc/tif file (from EPU/SerialEM) associated with a data collection session and launches Relion 4 or Scipion 3 pipeline.
a modern, open library for the analysis of molecular dynamics trajectories
a program that is used for including solvation effects in biological systems, such as proteins, using an atomic model of the protein. This is done by solving the Poisson-Boltzmann equation in a dielectric medium, including distributed point charges on a grid.
a pipeline for the automated detection of membrane-bound proteins in cryo-electron tomograms. It utilizes the geometry of a pre-segmented membrane to reduce the complexity of the detection task.
a tool for membrane segmentation in 3D for cryo-electron tomography (cryo-ET).
(Minimal Ensemble Search) a genetic algorithm used to identify the minimal ensemble required to best fit experimental data. The simulations provide an ensemble of molecular models from which a SAXS curve is calculated and compared to the experimental curve. Written by Martin Pelikan and Michal Hammel at Lawrence Berkeley Laboratory.
Keywords:
SAXS
Other
a software package for visualization and analysis of molecular structures comprising AutoDockTools (ADT): a graphical front-end for setting up and running AutoDock; Python Molecule Viewer (PMV); and Vision: a visual-programming environment for building networks describing novel combinations of computational methods and yielding new visualizations of their data.
a series of software tools for docking flexible ligands into receptors with selective flexibility, comprising: 1) AutoDockFR: a docking engine using the AutoDock4 forcefield; 2) AutoGridFR: a graphical user interface for setting up docking boxes; 3) AutoSite: a ligand binding site detection and characterization program.
an interactive graphics application for molecular modeling, fitting, and refinement of protein structures from X-ray crystallography developed by Bradley Smith as an Open Source project while working for Rigaku/MSC Inc. A particular focus of the MIFit software is the efficient solution and analysis of protein:ligand complexes.
a self-supervised molecular pattern mining and particle localization in situ.
a probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data, and identifies differentially regulated isoforms or exons across samples. MISO is installed as a standalone program and as a module within python.
(Metropolis Monte Carlo) a program for the simulation of molecular assemblies in the canonical, grand-canonical and isothermal-isobaric ensembles employing several convergence acceleration techniques (e.g., force-biased displacement, extension-biased and local torsion changes, preferential selection of solvent to be moved, cavity-biased insertion, virial-biased volume change).
an ultra fast and sensitive sequence search and clustering suite
(Multiscale Modeling Tools for Structural Biology) a collection of perl-based user-level utilities as well as programming libraries for multiscale protein structure modeling. Intended applications include protein structure prediction, loop modeling, structure refinement, and structure evaluation/scoring.
an automatic atomic model building program for cryo-EM maps.
a program to fit the extended model free spectral density function to NMR spin relaxation data. The program can analyze the spin-lattice relaxation rate constant (R1), the spin-spin relaxation rate constant (R2), and the heteronuclear steady-state {1H}-X nuclear Overhauser effect (NOE) for any combination of 13C and 15N spins at up to five static magnetic fields.
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NMR
a tool used for homology or comparative modeling of protein three-dimensional structures. From a sequence alignment with known related structures, MODELLER automatically calculates a model containing all non-hydrogen atoms using comparative protein structure modeling by satisfaction of spatial restraints. It can also perform de novo modeling of loops in protein structures and optimize various models of protein structure with respect to a flexibly defined …
a program for comparative modeling of RNA 3D structures.
a novel program developed to allow the determination of alignment tensor parameters for individual or multiple domains in macromolecules from residual dipolar couplings and to facilitate their manipulation and construct low-resolution models of macromolecular structure.
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NMR
a universal toolkit rapid, automated location and characterization of channels and pores in molecular structures. The core of the MOLE algorithm is a Dijsktra path search algorithm, which is applied to a Voronoi mesh. It can explore large molecular channels, complex networks of channels, and molecular dynamics trajectories that requires analysis of a large number of snapshots.
a tool that enables quick import and visualisation of structural biology data inside of Blender.
a molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules.
(MOLecular PHYlogenetics) a computer program package for molecular phylogenetics.
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Other
a protein structure analysis platform offering quality validation for 3D structures of proteins, nucleic acids and complexes.
a program for creating schematic or detailed, publication-quality molecular graphics images from molecular 3D coordinates, usually, but not exclusively, protein structures.
a pipeline for molecular replacement protein structure solution using X-ray data. The software package includes a database and a set of programs for the structure solution.
a package for processing film and image plate data.
a multi-GPU program that corrects beam-induced sample motion on dose fractionated movie stacks. It implements a robust iterative alignment algorithm that delivers precise measurement and correction of both global and non-uniform local motions at single pixel level across the whole frame, suitable for both single-particle and tomographic images.
a multi-GPU program that corrects beam-induced sample motion on dose fractionated movie stacks. It implements a robust iterative alignment algorithm that delivers precise measurement and correction of both global and non-uniform local motions at single pixel level across the whole frame, suitable for both single-particle and tomographic images.
a program that corrects whole frame image motion recorded with dose fractionated image stacks.
a high performance and widely portable implementation of the Message Passing Interface (MPI) standard.
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Other
a tool for membrane flatten and visualization.
a system that determines the structure of macromolecular assemblies. The approach has been to study specimens with some form of symmetry, such as crystals or helical and icosahedral particles, using programs suitable for many kinds of 2-D and 3-D analysis.
a PDB preparation tool for use with ProSmart or for Molecular Replacement
(multiple sequence comparison by log-expectation) a public domain multiple alignment software for protein and nucleotide sequences.
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Other
a molecular manipulation language, NAB (Nucleic Acid Builder) that interfaces to SFF (Simple Force Field) in Amber.
a stand-alone program that calculates the accessible area of a molecule from a PDB format file.
a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
a commandline tool, written in BASH, that sets up and runs a MDFF (molecular Dynamics Flexible Fit) simulation in a semi automatic manner, using only the input PDB file and input density file.
a Python library for n-dimensional image visualization, annotation, and analysis.
Keywords:
Visualization
a plugin for napari to aid in tomogram visualisation and annotation.
a multi-purpose text editor for the X Window System, which combines a standard, easy to use, graphical user interface with thorough functionality and stability.
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Other
an HDF5 read plugin for XDS. Neggia presents HDF5 data to XDS in a fully parallelized way, directly and without interconversion and speeds up the processing of HDF5 data.
an open source software to analyse NMR relaxation dispersion data of either CPMG or R1p (R1rho) dispersion experiments. The graphical interface enables simple management of large experimental data sets and simple and automated analysis. NESSY autamatically calculates effective transverse relaxation rate (R2eff) and performs model selection between different relaxation dispersion models.
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NMR
a simple command-line program that allows you to submit a single file of FASTA sequences over an internet connection to the NCBI BLAST databases. Searches are submitted through the client to the NCBI servers and do not need to download the databases locally (also called netblast and blastcl3).
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Other
a Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.
a new version of Sparky renamed because NMRFAM, through the generous allowance of Tom Ferrin and Tom Goddard of UCSF, has taken over the original Sparky for continuous development to support advances in the biomolecular NMR field.
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NMR
a tool for NMR processing, visualization and analysis that Integrates code of NMRFx Processor, Structure and additional tools
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NMR
a software for processing multi-dimensional NMR spectra featuring quality and performance to handle complex data analyses.
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NMR
NMRFx Structure can be used to generate and analyze macromolecular structures and predict chemical shifts.
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NMR
a python module for reading, writing, and interacting with the spectral data stored in a number of common NMR data formats.
a set of comprehensive facilities for Fourier processing of spectra in one to four dimensions, as well as a variety of facilities for spectral display and analysis. This is the official NMRScience version of NMRPipe.
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NMR
an easy-to-use software package for the two-dimensional lineshape analysis of titration experiments.
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NMR
a tool used to visualize and Analyze Nuclear Magnetic Resonance Data.
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NMR
a tool used to visualize and Analyze Nuclear Magnetic Resonance Data.
Keywords:
NMR
a software suite for the modelling of large conformational changes of 3-D protein structures under the constraint of a low resolution electron density map. Norma is used to interpret electron microscopy data using atomic scale resolution structural models and perform flexible fitting on new cases without encountering major technical difficulties.
a program that provides 3D-CTF correction for cryo-electron tomography
a Perl program that allows PyMOL to display atomic models of nucleic acids in a highly simplified representation.
a program to generate schematic diagrams of protein-DNA interactions. The program works for any single- or double-stranded protein-DNA, DNA-ligand and protein-RNA complexes.
NuFold is a state-of-the-art method designed for predicting 3D RNA structures, leveraging deep learning for high accuracy and reliability. This tool is particularly useful for biologists and bioinformatics researchers focusing on RNA function and structure.
a new user-friendly method built for automatic Δχ-tensor determination.
Keywords:
NMR
a model building application for X-ray crystallography.
a fast and simple python module and program to estimate local scaling of cryo-EM maps, to approximate relative occupancy and/or resolution, and optionally to equalize the map according to occupancy while suppressing solvent amplification.
an easy-to-use program containing everything you need to solve, refine and finish small-molecule crystal structures using an intuitive user interface, honed over ten years of development.
a high-resolution de novo Structure Prediction from Primary Sequence
a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.
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Other
a trainable, memory-efficient, and GPU-friendly PyTorch reproduction of DeepMind's AlphaFold 2.
(Open Java Development Kit) a free and open source implementation of the Java Platform, Standard Edition (Java SE).
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Other
a high performance toolkit for molecular simulation that can be used either as a stand-alone application for running simulations or as a library you call from your own code.
an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available.
an open-source software designed for conducting molecular dynamics (MD) simulations of the human nucleus. This software streamlines the process of setting up whole nucleus simulations through just a few lines of Python scripting.
an electronic structure program package that is a flexible, efficient, and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules.

Restriction: available to academic users who register on the ORCA website / non-profit users who email orca.license@cec.mpg.de or info@faccts.de & submit confirmation to SBGrid.
(Prediction of ALignmEnt from Structure) a software for the analysis of residual dipolar couplings and for the prediction of the magnitude and orientation of a sterically induced alignment tensor from a solute's (protein/nucleic acid/oligosaccharide) three-dimensional shape.
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NMR
a library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language. pandas is installed as a module within python.
a python module for calculating paramagnetic effects in NMR spectra of proteins. This currently includes fitting of paramagnetic susceptibility tensors to experimental data associated with pseudocontact shifts (PCS) residual dipolar couplings (RDC), paramagnetic relaxation enhancements (PRE) and cross-correlated relaxation (CCR). A GUI allows easy viewing of data and seamless transition between PCS/RDC/PRE/CCR calculations.
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NMR
a software package for single-particle EM image processing. It provides an integrated computing environment with comprehensive data analysis functions for particle selection, particle classification, 3D reconstruction and model evaluation. In addition, PARTICLE emphasizes on data visualization that enables the user to "see" the data throughout the process.
a Python package that automates structure preparation tasks for continuum electrostatics calculations. It can convert protein files in PDB format to PQR format. It can add a limited number of missing heavy atoms to biomolecular structures, determine side-chain pKas, placing missing hydrogens, optimize the protein for favorable hydrogen bonding, and assign charge and radius parameters from a variety of force fields.
a tool that identifies and assigns carbohydrate structures using only atom types and their 3D atom coordinates given in PDB-files. Looking up a translation table where systematic names and the respective PDB residue codes are listed, both assignments are compared and inconsistencies are reported.
a program suite that contains tools and examples for extracting data from many structure determination applications and assembles the data into mmCIF format for wwPDB deposition.
an easy to use application that fixes problems in Protein Data Bank files in preparation for simulating. Fixes include: adding missing heavy or hydrogen atoms, building missing loops, convert non-standard residues to their standard equivalents, deleting unwanted heterogens or chains from the model, and building a water box for explicit solvent simulations.
a command-line tool from PDBe EMBL-EBI for generating images of macromolecular structures from mmCIF or binary CIF structure files based on Mol*.
a program that refines any structural model you are working on, by optimising REFMAC refinement and by partial model rebuilding. The process is fully automated so you only need to provide an initial structure model and your reflection data.
a C/C++ application developed as a coordinate and protein NMR restraint converter. This user-friendly tool provides an integrated set of computational methods for protein NMR restraint analysis and structure quality assessment, relabeling of prochiral atoms with correct IUPAC names, and analysis of atomic position consistency based on their convergence across a protein NMR ensemble.
a swiss army knife for manipulating and editing PDB files.
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Other
a set of tools used by the PDB for processing and checking structure data.
(Particle Estimation for Electron Tomography) a package for aligning and averaging particles in 3-D subvolumes extracted from tomograms. If PEET and IMOD are both installed, most PEET operations are available from the eTomo graphical user interface in IMOD. PEET is written in Matlab and a compiled version is distributed along with the Matlab runtime environment needed to run it.
a tool that performs orientation searches and positional refinement of icosahedral viruses.
a Fortran- or C-callable, device-independent graphics package for making simple scientific graphs.
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Other
a program that computes phase angles for diffraction data from macromolecular crystals with programs for merging and scaling of native and derivative data sets; analyzing difference statistics; computing Patterson and electron density maps; searching for peaks; refining heavy atoms (or protein domains as rigid groups); computing phases by MIR, SIR, SAS, SIRAS, MIRAS, or from atomic coordinates for an input model; noncrystallographic symmetry averaging; …
(Python-based Hierarchical Environment for INtegrated Xtallography) a software suite for the automated determination of molecular structures using X-ray crystallography and other methods.
a software package for image processing of helical macromolecular complexes.
a free package of software programs for inferring phylogenies.
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Other
a tool that performs conversions of spectra from NMRPipe to XEASY format. It can read the ASCII file with header information, which is produced with "showhdr -verb filename".
Keywords:
NMR
(Protein-Ligand Interaction Profiler) a tool for automated detection and visualization of relevant non-covalent protein-ligand contacts in 3D structures. Available as a stand alone application or a web service.
a tool that infers undirected graphical models to describe coevolution and covariation in families of biological sequences. With a multiple sequence alignment as an input, plmc can quantify inferred coupling strengths between all pairs of positions (couplingsfile output) or infer a generative model of the sequences for predicting the effects of mutations or designing new sequences (paramfile output).
a multipurpose X11 plotting program that specializes in contour plots but can also handle 2D and 3D plots. The plot-types supported are: contour plots (rectangular grid, as well as triangular mesh), 2D line and scatter plots (x-vs-y), 3D surface , line and scatter plots, vector plots, probability plots, histograms, barcharts.
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Other
a GNU package containing software for programmers and technical users. Its centerpiece is libplot, a powerful C/C++ function library for exporting 2-D vector graphics in many file formats, both vector and raster. It can also do vector graphics animations. plotutils also contains command-line programs for plotting scientific data, many of which use libplot to export graphics.
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Other
an open source library for free energy calculations in molecular systems that works with some of the most popular molecular dynamics engines. Perform free energy calculations as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation-based steered MD.
a software suite for multidimensional NMR and 3D structure calculation of biomolecules.
Keywords:
NMR
a tool designed to build mechanistic models - i.e. models that simulates a biological process.
a newly designed NMR chemical shift guided protein structure alignment method to generate protein templates with the best matched local structure from the Protein Data Bank.
Keywords:
NMR
(Persistence of Vision Raytracer) a high-quality, totally free tool for creating stunning three-dimensional graphics. It is available in official versions for Windows, Mac OS/Mac OS X and i86 Linux. The source code is available for those wanting to do their own ports. POVRAY was originally written by David Kirk Buck and Aaron A. Collins.
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Other
a Python package and simple command-line program to automatically fit high-resolution atomic structures in cryo-EM densities.
a graphical interface to a collection of applications for the analysis and visualization of multidimensional data, with a focus on data from 3D optical microscopy and electron tomography. IVE (Image Visualization environment) is the core set of software libraries that are the foundation for the tools in Priism.
a widely used program that designs PCR primers (PCR = "Polymerase Chain Reaction"). Primer3 can also design hybridization probes and sequencing primers.
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Other
an efficient protein multiple sequence alignment program, which has demonstrated a statistically significant improvement in accuracy compared to several leading alignment tools.
Keywords:
Other
an application to evaluate atomic packing, either within or between molecules. It generates “contact dots” where atoms are in close contact. Probe reads atomic coordinates from protein databank (PDB) format files and writes dot-lists for inclusion in a kinemage file.
a program for checking the stereochemical quality of a protein structure, producing a number of PostScript plots analyzing its overall and residue-by-residue geometry.
a protein structural dynamics analysis software package. ProDy is installed as a module within python.
a program for the ultimate protein least squares fitting.
a program that creates fragments for Rosetta. For commercial users, Biosof LLC (www.bio-sof.com) offers additional customization and data analysis of PROFphd.
(PROfile Multiple Alignment with predicted Local Structure) a progressive method for aligning multiple protein sequences, with enhanced profile information from database searches and secondary structure prediction.
a tool that predicts the pKa values of ionizable groups in proteins (version 3.0) and protein-ligand complexes (version 3.1 and later) based on the 3D structure.
a threading-based protein structure prediction system.
a deep learning based protein sequence design method.
a trainable PyTorch reproduction of AlphaFold 3.
a general purpose program for protein design, to redesign entire proteins or functional sites such as ligand-binding pockets. It uses a physics-based energy function and a stochastic method to search sequence and conformation space and allows users to directly select mutations that increase ligand binding free energy or ligand specificity. It can perform constant-pH Monte Carlo, which yields acid/base constants or pKa’s.
a Python library for structural bioinformatics, protein engineering, and machine learning. It offers tools for file handling, database access, protein representation, structure analysis, property calculation, and geometric operations.
a system that includes programs and shell scripts for electron tomography of thin specimens, providing an interactive graphical tool for fast initial alignment of a tilt series, shell scripts for the more time consuming refinement, and some other useful image manipulation utilities.
a tool that converts a protein sequence alignment in BLAST, CLUSTAL or MSF format to a property file used to map the sequence conservation onto the structure of a protein using the GRASP program or the MOLMOL program or the PyMOL program. A pseudo-PDB file with the sequence conservation score in place of the temperature factor is also provided, to use with programs such …
a python package for processing x-ray scattering data, first developed at the X9 beamline at NSLS, but revised multiple times and now in use at the LiX beamline at NSLS-II.
Keywords:
SAXS
Other
a set of Python modules and command-line utilities for electron microscopy of biological samples.
a Python library for the estimation, validation and analysis Markov models of molecular kinetics and other kinetic and thermodynamic models from molecular dynamics (MD) data.
a Python-based GUI program for indexing power spectra of helical assemblies.
a widely used molecular visualization package developed by Warren DeLano, now maintained by Schödinger, LLC. This installation includes official incentive builds of PyMOL.

Restriction: available to non-profit groups in North America, Europe, Asia, and Australia.
a python package that offers RMSD calculations on large sets of structures, especially large pairwise RMSD matrices through multiple algorithmic implementations.
an interactive Python-based interface to the powerful Rosetta molecular modeling suite that enables users to design their own custom molecular modeling algorithms using Rosetta sampling methods and energy functions.
a python module that makes it easy to read and manipulate genomic data sets. It is a lightweight wrapper of the htslib C-API; it provides facilities to read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well as access to the command line functionality of the SAMtools and BCFtools packages. Pysam is installed as a module within python.
a general-purpose, interpreted, object oriented, high-level dynamic programming language that emphasizes code readability. Its syntax allows programmers to express concepts in fewer lines of code than in C++ or Java, thus allowing programmers to work more quickly and integrate their systems more effectively.
Keywords:
Other
a software toolkit and library of routines for the analysis and manipulation of macromolecular structural models, implemented in the Python programming language.
a software for template matching on tomographic electron microscopy data.
a tool that unifies standard tomogram processing steps in a single python-based toolbox. For subtomogram averaging, we implemented an adaptive adjustment of scoring and sampling that clearly improves the resolution of averages compared to static strategies.
a GPU accelerated python module to significantly improve the speed and sensitivity using template matching to detect macromolecules from tomograms.
a collection of programs for modeling multi-conformer protein structures.
a "quick" evaluation of steric packing in protein structures. Amino acid side chains are not represented in full atomic detail, but instead uses one or more averaged centers of interaction per residue. Side chain packing quality is determined from the spherical space available to each residue. Empirical pairwise residue contact potential can be used to estimate the correctness of model protein structures.
a program that detects contiguous stretches of hydrophobic surface area on the surfaces of macromolecules.
a comprehensive, platform-independent, user-friendly, and complete software package that enables efficient, reliable, highly automated, and accurate analysis of high-throughput capillary electrophoresis-detected nucleic acid chemical probing experiments.
a free software environment for statistical computing and graphics.
Keywords:
Other
a program to assist in aesthetic drawings of RNA secondary structures. It is primarily aimed at drawing consensus diagrams, but can also draw single RNA molecules.
a software tool allowing the estimation of the dose absorbed in a macromolecular crystallography diffraction experiment.
a small tool to randomize phases of a 3D map in a given resolution zone. The randomization can be used to test bias in the refinement of atomic models into a map.
a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images.
(Protein NMR backbone resonance assignment) a tool that uses structure-based chemical shift predictions to solve the backbone resonance assignment problem in protein NMR spectroscopy to enable rapid determination of highly accurate assignments on the basis of minimal experimental datasets, even for spectroscopically challenging proteins.
Keywords:
NMR
a set of tools for generating high quality raster images of proteins or other molecules.
a tool that allows for semi-automated building of RNA structure within Coot.
a collection of cheminformatics and machine-learning software written in C++ and Python.
a fast, versatile and program for docking ligands to proteins and nucleic acids.
Keywords:
Other
a software tool for analyzing different conformations in heterogeneous cryo-EM and cryo-ET datasets. RECOVAR can reconstruct high-resolution volumes, estimate conformational density and low free-energy motions, and automatically identify subsets of images with a particular volume feature.
a residual dipolar coupling analysis tool. For-profit users interested in using this tool should contact Homayoun Valafar at hvalafar@gmail.com to inquire.
Keywords:
NMR
a program for adding hydrogens to a Protein DataBank (PDB) molecular structure file. Hydrogens are added in standardized geometry with optimization of the orientations of OH, SH, NH3+, Met methyls, Asn and Gln sidechain amides, and His rings. Both proteins and nucleic acids can be processed. HET groups can also be processed as long as the atom connectivity is provided.
a program that carries out rigid body, tls, restrained or unrestrained refinement against Xray data, or idealisation of a macromolecular structure. It minimises the coordinate parameters to satisfy either a Maximum Likelihood or Least Squares residual. It also produces an MTZ output file containing weighted coefficients for SigmaA weighted mFo-DFcalc and 2mFo-DFcalc maps, where missing data have been restored.
a molecular design tool for de novo design, scaffold hopping, R-group replacement, linker design, molecule optimization, and other small molecule design tasks.
a software package designed for the study of molecular dynamics by NMR data analysis.
Keywords:
NMR
(REgularised LIkelihood OptimisatioN) a stand-alone computer program for Maximum A Posteriori (MAP) refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy.
a tool that converts Star Files from RELION 4.0 to Dynamo Table
a RELION tool with block-based reconstruction modifications.
a RELION 4 tool with support for composite masks
a simple python script which enables one to follow the progress of 2D/3D classification and refinement in RELION in real time.
a set of additional tools for subtomogram analysis in Relion tomo.
a collection of scripts for cryoEM data collection and analysis
a Python Utilities program for converting between Cryosparc and Relion File Formats
a tool that converts PDB files between PDBv2.3 and PDBv3.2 formats. It can accurately and rapidly convert in either direction: old to new OR new to old. Atom records of type ATOM, HETATM, TER, ANISOU, SIGATM, SIGUIJ, and LINK are converted, as are DNA residue names (e.g., A, C, T, G of v2.3 cf. DA, DC, DT, DG of v3.2).
a suite of programs for molecular replacement calculations. It currently consists of two major programs, GLRF for rotation function calculations and TF for translation function calculations. In addition, a small program (ANGCAL) is a convenient tool for conversions between angles and matrices.
(Resolution Map) a Python (NumPy/SciPy) application with a Tkinter GUI. It is an easy to use software package for computing the local resolution of 3D density maps studied in structural biology, primarily electron cryo-microscopy (cryo-EM). ResMap has a both a GUI (window) and a command line interface.
a program for denoising cryogenic electron microscopy images with a convolutional neural network.
a tool for protein hallucination and inpainting with RoseTTAFold.
an open source method for structure generation, with or without conditional information (a motif, target etc). It can perform a whole range of protein design challenges.
a program to detect molecular motions by automatic electron density sampling.
a code for performing RING-MaP and PAIR-MaP analysis.
a program for measuring the resolution of single-particle reconstructions.
Keywords:
Other
a tool. that calculates Rpim for merging, which HKL (scalepack) does not. There's no official manual right now but you can see Cell 147, 199-208 for more information.
a modular toolkit developed to deal with RNA structure probing and post-transcriptional modifications mapping high-throughput data. Toolkit will help with automatic reference transcriptome creation, automatic reads preprocessing (adapter clipping and trimming) and mapping, scoring and data normalization, and accurate RNA folding prediction by incorporating structural probing data.
a visualization tool that displays/edits 2-dimensional diagrams of RNA/DNA secondary structures with tertiary interactions created by RNAView. It generates standard molecular representations (e.g. tRNA cloverleaf structures) or any structural representations by rearranging various parts (e.g helices and single strands) of the RNAView 2D diagrams. RNA motifs are rapidly identified and classified with the base pair annotation and the 2D graphic display.
a complete package for RNA and DNA secondary structure prediction and analysis.
a tool that quickly displays the secondary structure of RNA/DNA with tertiary interactions. It is fully implemented with Leontis and Westhof's ( RNA (2001) 7, 499-512), convention for the edge-to-edge hydrogen bonding interactions.
(Refinement and Optimization via Machine lEarning for cryo-EM) a parallel computing software system dedicated for high-resolution cryo-EM structure determination and data analysis, which implements advanced machine learning approaches in modern computer sciences and runs natively in an HPC environment.
a software suite for modeling macromolecular structures and for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions.
a program that provides an accurate prediction of protein structures and interactions using a 3-track network.
a biomolecular structure prediction neural network that can predict a broad range of biomolecular assemblies.
a program for the fitting of atomic models into electron density maps derived from x-ray crystallography or electron microscopy (EM).
a tool that supports real-space simulated annealing refinement with X-ray data using an electron density function that is resolution-dependent, so that it accurately models a medium resolution map. When combined with TNT’s Geometry or CNS, full stereochemical refinement is possible. It can quickly pre-refine a protein structure during or after model building, or to completely refine structures with high non-crystallographic symmetry, that have good …
an integrated development environment (IDE) for R that includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.
Keywords:
Other
a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write.
Keywords:
Other
a fast, versatile, and open-source program for docking ligands to proteins and nucleic acids.
(Sequence Alignment and Modeling system) a collection of tools for creating, refining, and using linear hidden Markov models for biological sequence analysis.
(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.
a 2D image display and analysis program, specifically designed for single-particle EM.

Professor Maofu Liao, Liao Lab, Cell Biology, HMS.
a program suite used to create atomistic models of molecular systems and to compare scattering data from these models directly to experimental data.
Keywords:
SAXS
Other
a set of tools used to create atomistic models of molecular systems and to compare scattering data from these models directly to experimental data plus “courtesy modules,” which include the molecular dynamics package NAMD, the scattering calculators Cryson and Crysol, and the program Hydropro for calculating hydrodynamic properties.

Restriction: available to nonprofit users who register with EMBL and send confirmation to SBGrid.

Keywords:
SAXS
Other
a plotting facility for SAXS-data, as well as a convenient tool to quickly generate plots for publication. Saxsview shows 1D-data in .dat, .int, .fit and .fir formats of the ATSAS package, the cansas .xml format (v1.0), as well as .csv files.
Keywords:
SAXS
Other
an application for managing an SBGrid software installation. Users can choose a subset of applications for installation on their laptops or desktops or configure site installations for clusters, servers or cloud resources. This version is the command-line interface. A graphical version is available for download on the SBGrid wiki : [https://sbgrid.org/wiki/client_downloads](https://sbgrid.org/wiki/client_downloads) .
Keywords:
Other
a JAVA-based application for basic analysis of SAXS datasets. Scatter is developed by Robert Rambo at the Diamond Light Source (Didcot, UK). The program was previously developed at the SIBYLS beamline (12.3.1) of the Advanced Light Source, Berkeley, CA.
Keywords:
SAXS
Other
a suite of programs for sequence alignment: 1) aln: Pairwise alignment of biological sequences supporting spliced alignment procedures; 2) swg: locally aligns a pair of DNA or protein sequences by Smith-Waterman-Gotoh algorithm; 3) prrn: global multiple alignment of a set of protein or DNA sequences by doubly-nested iterative refinement method; 4) phyln: UPGMA or NJ method to make a phylogenetic tree from a multiple …
Keywords:
Other
a suite of tools for drug discovery.

Restriction: shared tokens available to non-profit academic labs in North America and Australia as an add-on option
an image processing framework to obtain 3D models of macromolecular complexes using 3D EM that allows you to execute workflows combining different software tools, while taking care of formats and conversions.
an interactive multi-resolution docking and visualization program for low-resolution density maps and atomic structures.
a program for prediction of protein side-chain conformations.
a program for prediction of protein side-chain conformations.
a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny.
a structure refinement and validation for crystallography and single particle analysis.
a tool that converts raw sequencing files into mutational profiles, creates SHAPE reactivity plots, and provides extensive diagnostic information useful for experiment analysis and troubleshooting.
Keywords:
Other
a completely rewritten version of our ShapeMapper for reading out the results of an RNA chemical probing experiment by massively parallel sequencing that integrates careful handling of all classes of adduct-induced sequence changes, sequence variant correction, basecall quality filters, and quality-control warnings to identify RNA adduct sites.
an automated structure solution pipeline built around the heavy-atom refinement and phasing program SHARP, the substructure determination program SHELXD, the density modification program SOLOMON and the model building programs BUCCANEER and ARP/wARP. It allows fully automated structure solution by experimental phasing, from merged reflection data to an initial model, without any user intervention.

Restriction: available to nonprofit users who register with Global Phasing and copy license file to /programs/local/autosharp/autosharp_license.
a set of programs for macromolecular phasing. SHELXC provides a simple and fast way to set up the files for the programs SHELXD (heavy atom location) and SHELXE (phasing and density modification) for macromolecular phasing by the MAD, SAD, SIR and SIRAS methods. hkl2map provides a simple user interface to SHELX and is installed separately.

Restriction: available to nonprofit users who register for SHELX & submit confirmation to SBGrid.
a set of programs for macromolecular phasing. SHELXC is designed to provide a simple and fast way of setting up the files for the programs SHELXD (heavy atom location) and SHELXE (phasing and density modification) for macromolecular phasing by the MAD, SAD, SIR and SIRAS methods. hkl2map provides a simple user interface to SHELX and is installed separately.

Restriction: this version of SHELX is obsolete and has been replaced by SHELX-2013.
a cute graphical user interface for SHELXL.
a program that predicts the backbone and side chain 1H, 13C and 15N chemical shifts for proteins using their structural (PDB) coordinates as input.
Keywords:
NMR
a tool for mitigating local over-fitting during single particle reconstruction.
an automated particle selection system for electron microscopy. The application was written by James Chen in Niko Grigorieff laboratory at Brandeis.
(Single-particle IMage Processing Linux Engine) does ab initio 3D reconstruction (programs cluster & origami), heterogeneity analysis (programs cluster, origami & cycler), and high-resolution refinement (programs align, reconstruct, automask & cycler).
a collection of utilities designed to help setting up and analyze molecular simulations.
SIREn is a toolkit for analyzing heterogeneity in 3D volume ensembles generated via cryo-EM. SIREn performs automated detection of structural blocks to allow model-free detection of heterogeneity, and additionally includes a 3D Convolutional Neural Network (CNN) to predict binarization thresholds for 3D density maps.
a program package for modeling of atomic resolution structures into low-resolution density maps. The software supports both rigid-body and flexible docking using a variety of fitting strategies.
is a free and open-source platform for analyzing and understanding medical image data.
an R package that provides functions for inferring continuous, branching lineage structures in low-dimensional data. Designed to model developmental trajectories in single-cell RNA sequencing data and serve as a component in an analysis pipeline after dimensionality reduction and clustering, Slingshot is flexible enough to handle arbitrarily many branching events and allows for the incorporation of prior knowledge through supervised graph construction.
a tool for detecting unlabeled macromolecules in 2D Cryo-EM images of cells that uses high-resolution template matching.
a fork of AutoDock Vina that is customized to better support scoring function development and high-performance energy minimization. smina is maintained by David Koes at the University of Pittsburgh and is not directly affiliated with the AutoDock project.
a computer program for the determination of the anomalously scattering substructures of selenomethionyl-substituted proteins containing as many as 160 Se sites. Based on Shake-and-Bake (a dual-space direct-methods procedure).
a program to construct an atomic solvent environment model for a given atomic macromolecule model (solute) for use in molecular dynamics simulations.
a program that can automatically search for heavy atom sites, calculate initial phases and perform density modification.
a 6D global search and multi-start optimization molecular replacement package.
a graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers.
Keywords:
NMR
(single particle analysis for resolution extension) an image processing environment with a particular emphasis on transmission electron microscopy (TEM) structure determination. It includes a graphical user interface that provides a complete graphical programming environment.
a tool that provides a fast way to visualize NMR spectrum and peak data. It supports 2D and 3D graphical display modes for multidimensional and simple 1D spectra. Can automatically import spectra and peaks from many different file formats without user intervention. Spectra may be frequency referenced and superposed within the program.
Keywords:
NMR
(SParx for HIgh Resolution Electron microscopy) a tool for cryoEM using statistical resampling to attain quality assessment and result reproducibility. Includes movie frame alignments (movie), CTF estimation of raw electron micrographs (cter), picking/stack creation (window), reproducible 2-D classification (isac), reproducible initial model generation (viper), automatic gold-standard 3-D refinement (meridien), local resolution estimation and filtering (localres), and up to the 3-D sorting of different conformational …
(System for Processing Image Data from Electron microscopy and Related fields) a large image processing suite for electron microscopy.
a graphical user interface for executing SPIDER batch files and other programs, Spire offers a way to manage and organize the many output files created by SPIDER during reconstruction projects.
a tool designed to correct for the preferred orientation problem in cryoEM by self-supervised deep learning, by recovering missing information from well-sampled orientations in Fourier space.
(Single Particle Reconstruction from Images of kNown Geometry) a single-particle based helical reconstruction package for electron cryo-micrographs used to determine 3D structures of either highly ordered or less ordered specimens.
is a powerful scientific environment written in Python, for Python, and designed by and for scientists, engineers and data analysts.
Keywords:
(Sequence Read Archive Toolkit) a collection of tools and libraries for using data in the INSDC Sequence Read Archives.
Keywords:
(Sequence Search and Alignment by Hashing Algorithm) a pairwise sequence alignment program designed for the efficient mapping of sequencing reads onto genomic reference sequences. SSAHA2 reads of most sequencing platforms (ABI-Sanger, Roche 454, Illumina-Solexa) and a range of output formats (SAM, CIGAR, PSL etc.) are supported. A pile-up pipeline for analysis and genotype calling is available as a separate package.
Keywords:
Other
a program that generates publication-quality protein secondary structure diagrams from three-dimensional protein structures. To depict relationships between secondary structure and other protein features, diagrams can be colored by conservation score, B-factor, or custom scoring.
a set of DNA sequence assembly, editing and analyzing tools developed at the Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
Keywords:
Other
(STructural Alignment of Multiple Proteins) a suite of programs to compare and align protein 3-D structures. It will multiply align structures and produce a corresponding sequence alignment with confidence values associated with each aligned position. It will also search a database of protein structures to identify structurally similar proteins and includes a number of utility programs for the manipulation of protein structures.
a Python implementation of the STAR file format designed principally for compatibility with RELION format STAR files. It allows STAR files to be created and opened easily using a very simple API, exposing data blocks as pandas DataFrame objects.
a package implemented in Python to manipulate Relion star files including counting, modifying, plotting, and sifting the data.
a subtomogram averaging workflow written in MATLAB for performing a number of subtomogram averaging tasks including template matching, high-resolution alignment and averaging, and classification.
a program to recognize secondary structural elements in proteins from their atomic coordinates.
(Subtomogram averaging scripts with TOM toolbox or Subvolume processing scripts with the TOM toolbox) a collection of scripts for a pipeline for subvolume alignment and averaging of electron cryo-tomography data.
a tool that uses the alignment results from the software application Unblur to calculate movie frame sums.
a pipeline that uses data obtained from ShapeMapper to model RNA secondary structures, including pseudoknots; identify de novo regions with well-defined and stable structures; and visualize most probable and alternative helices.
a flexible, modular software package intended primarily for the processing of transmission electron micrographs. One of several applications developed by Automated Molecular Imaging Group at The Scripps Research Institute.
a pipeline of tools to generate robust open mesh surfaces from voxel segmentations of biological membranes using the Screened Poisson algorithm and calculate morphological features including curvature and membrane-membrane distance using pycurv's vector voting framework with tools to convert these morphological quantities into morphometric insights.
a program that calculates exact accessible surface area, molecular surface area and average curvature of molecular surface for macromolecules. The program also analyzes cavities in the protein interior inaccessible to solvent from outside.
a program that generates surfaces, density contours and gap regions from coordinate data supplied in a PDB file.
a program that calculates solvent accessible area that is defined by a probe as it rolls on the surface of the molecule. Thus use of a zero radius probe will give the Van der Walls surface area.
an application that provides a user friendly interface allowing you to analyze several proteins at the same time.
a tool that predicts protein backbone and sidechain torsion angles from NMR chemical shifts
Keywords:
NMR
a neural network-based segmentation tool that automates the analysis of cytoskeletal structures in electron microscopy data accurately distinguishing individual filaments and membranes in complex cellular environments.
a multiple sequence alignment package that can be used to align sequences or to combine the output of your favorite alignment methods (Clustal, Mafft, Probcons, Muscle...) into one unique alignment (M-Coffee).
Keywords:
Other
a tool that helps flexible-fitting and refinement of atomic models into cryo-EM maps.
a program that allows the determination of rotational diffusion from three-dimensional structure coordinates and experimental 15N relaxation data, and now allows a rigorous model-free analysis of local internal mobility affecting backbone amides, from 15N {R1,R2,nOe} relaxation rates in the presence of an isotropic or anisotropic rotational diffusion tensor.
Keywords:
NMR
a system that cleans up raw data files and converts them to pdf format with LaTex. Offers an easy way to get up and running with the TeX document production system.
Keywords:
Other
a program for the simultaneous superpositioning and analysis of multiple macromolecular structures via the method of maximum likelihood (ML).
a particle-filter framework for robust cryoEM 3D reconstruction.
an open source suite of classes and programs implemented in C++ for single particle electron microscopic image processing.
a graphical user interface for picking particles from image tilt pairs for such applications as random conical tilt (RCT) and orthogonal tilt reconstruction (OTR). TiltPicker borrows its interface from Leginon and re-implements many of the tilt picking features of SPIDER WEB that can be run on modern computers.
a Python-based program package that can be used to efficiently detect and characterize significant conformational changes in simulated biomolecular systems.
a graphical front end to the diff program. It provides a side-by-side view of the differences between two files, along with several innovative features such as diff bookmarks and a graphical map of differences for quick navigation.
Keywords:
Other
an algorithm for sequence independent protein structure comparisons.
a package for fast tomographic reconstruction on multicore computers. Full resolution tomograms are generated at high speed on standard computers with no special system requirements.
a set of programs for cryo-tomography tilt-series alignment and subsequent tomographic reconstruction that take into consideration beam-induced sample motion, modeled by means of polynomial surfaces. TomoAlign comprises: 1) tomoalign, for alignment, to determine the basic parameters of the images (rotation, magnification, tilt) along with the polynomial coefficients that model the motion; 2) tomorec to calculate the tomogram from the tilt-series and takes into account …
a package for noise reduction in electron tomography with Anisotropic Nonlinear Diffusion.
a package for feature-preserving noise filtering in electron tomography.
a package for CTF determination and correction in electron cryotomography.
a tool that extends the cryoDRGN framework to cryo-ET by learning heterogeneity from datasets in which each particle is sampled by multiple projection images at different stage tilt angles.
an optimized software tool for fast feature-preserving noise filtering of large three-dimensional (3D) tomographic volumes on CPUs and GPUs. The tool is based on the anisotropic nonlinear diffusion method. It has been developed with special emphasis in the reduction of the computational demands by using different strategies, from the algorithmic to the high performance computing perspectives. TomoEED manages to filter large volumes in a …
a MATLAB package for managing the various preprocessing steps for taking raw data to reconstructed tomograms. TOMOMAN mainly acts as a set of wrapper scripts for external packages, managing the input and outputs of each external module to form a cohesive pipeline.
a software package with a modern graphical user interface to carry out the entire pipeline of cryoET and subtomogram averaging to achieve high resolution.
a software suite intended to assist users in segmenting membranes in tomograms, based on a local differential structure approach and on a Gaussian-like model of membrane profile.
a software package for segmenting membranes in tomograms. It is based on (1) a Gaussian-like model of membrane profile, (2) a local differential structure approach, and (3) anisotropic propagation of the local structural information using the tensor voting algorithm.
a tool that provides scripts for making cryo-electron tomography a bit easier.
a deep metric learning based particle picking procedure for cryo-ET
a pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Topaz includes methods for micrograph denoising using deep denoising models.
a program with added support for filament start-end coordinate picking (new options -f, -fp and -fl in the extract command extract.py) in Topaz, for subsequent helical reconstruction in RELION.
a collection of software tools for computational analysis of cryo-EM images developed by John Rubinstein/U Toronto
a software package for fully automated processing of cryo-EM data sets during data acquisition. TranSPHIRE transfers data from the microscope, automatically applies the common pre-processing steps, picks particles, performs 2D clustering and 3D refinement parallel to image recording. Importantly, TranSPHIRE introduces a machine learning-based feedback loop to re-train its internally used picking model to adapt to any given data set live during processing. This …
a tool for the conversion of microED data collected on TVIPS TemCam-F416, Thermo Fisher CetaD, and Thermo Fisher Falcon III to SMV crystallographic format (*.img)
an interactive multi-body protein-protein docking software that predicts the geometry of protein interactions through an intuitive real-time docking procedure with on-the-fly scoring
a software package for comprehensive analysis of hydrodynamic data from analytical ultracentrifugation experiments.
Keywords:
Other
a comprehensive data analysis software package for hydrodynamic data from analytical ultracentrifugation experiments. It is the latest multi-platform version of UltraScan, which replaced the UltraScan II distribution. UltraScan II development has stopped although it is still available.
Keywords:
Other
a tool used to align the frames of movies recorded on an electron microscope to reduce image blurring due to beam-induced motion. It reads stacks of movies that are stored in MRC/CCP4 format and generates frame sums that can be used in subsequent image processing.
a GPU-accelerated molecular docking program developed by DP Technology.
a program that performs automated NMR data analysis for protein 3D structure determination. It represents the result of more than a decade of innovative research performed in order to enable accurate, objective and highly automated protein structure determination by NMR.
a program designed to separate overlapping diffraction patterns from a set of crystals with slightly different orientations. The program can read x files from the HKL Package and CCP4 MTZ files. It can output data files from which the offending reflections have been removed. A case study for a dataset from an aggregate with three dominant subcrystals can be found here.
a tool designed for interactive fitting of high-resolution X-Ray crystallography models into Electron Microscopy reconstructions. It can also be used to fit two maps together (e.g., in tomography) or to perform Normal-modes calculations. UROX is deprecated, a new version named VEDA should be used instead.
a Swiss Army knife of crystallography tools. The installation includes the packages from RAVE, SBIN, X-UTIL, VOIDOO, DEJAVU and SPASM.
a visual environment developed to fit interactively atomic models into 3D reconstructions. Calculations are performed in reciprocal-space and the symmetry of the reconstruction is taken into account. The computations are fast and an entire EM reconstruction can be used.
a tool that identifies membrane proteins in cryo-EM micrographs by using the Segment Anything Model and integrating with cryoSPARC.
a computational tool using local vector based algorithm that can accurately identify the global and local alignment of cryo-electron microscopy (EM) maps.
a heterogeneous OpenCL implementation of AutoDock Vina.
a parallel molecular docking program that is a modified version of the very popular PC-based molecular docking program AutoDock Vina. VinaLC is a message passing interface and multithreading hybrid for parallel molecular docking of large databases on petascale high performance computing machines.
is a cryo‑EM density map sharpening tool that estimates the underlying atomic distribution of a protein from the density map and computes the corresponding radially averaged structure factor and density histogram.
a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
a combination of the X-PLOR structure determination program and VMD (Visual Molecular Dynamics) - a freely available molecular visualization program. This package allows manual manipulation of the protein structures to satisfy experimental NMR data, and can also be used to visualize the goodness of fit of a particular model to given restraints.

Restriction: available to users who register with the NIH & submit confirmation to SBGrid.
a tool for analysis of atomic neighborhoods in molecular structures using a Voronoi diagram of balls determined from the atomic model. It is especially suitable for processing three-dimensional structures of biological macromolecules such as proteins and RNA.
a tool that utilizes deep learning to perform volumetric electron microscopy image segmentations, both semantic and instance segmentation.
(Visualization Tool Kit) a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including scalar, vector, tensor, texture, and volumetric methods, as well as advanced modeling techniques such as implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.
a set of tools for cryo-EM and cryo-ET data processing including, among other tools: Warp, M, WarpTools, MTools, MCore, and Noise2Map.
a tool to visualize template matching results from Warp
a tool that searches PDB files for misidentified water molecules that should be modeled as cations.
a collection of Java programs for structural biology and NMR spectroscopy that analyze, annotate, parse, archive, and disseminate experimental NMR data deposited by authors worldwide into the PDB and BMRB.
Keywords:
NMR
a set of command line tools for sequence logo generation.
a protein verification tool from the WHAT IF program available as a free stand-alone program, complete with all source code.
a general protein analysis program.
a boxing program developed by James Conway.
a data management and workflow tool for the parallel determination of protein-ligand structures.
a two-dimensional molecule drawing program for Unix operating systems that can read and write MDL Molfiles, and read ChemDraw text and binary files, to allow sharing between XDrawChem and other chemistry applications, and it can create images in popular formats like PNG and EPS.
Keywords:
Other
(X-ray Detector Software) a software tool for processing single-crystal monochromatic diffraction data recorded by the rotation method.
a graphical user interface for processing diffraction data sets using XDS. It automates the data processing and generates graphical plots of various data set statistics provided by XDS and presenting new features of the dataset, such as radiation decay or the presence of pseudo-translational symmetry and/or twinning, using additional software. Generates intensity files suitable for CCP4, SHELX, and CNS.

Restriction: available to nonprofit users who register with HZB & submit confirmation to SBGrid.
a program for generating delta-CC1/2 values, for individual frames, or groups of frames, from a single dataset collected with the rotation method and processed by XDS.
a GUI (graphical user interface) for XDS designed to help both novice and experienced users; it enables XDS data processing without the command line and supplies additional graphical information in a simple, user-modifiable and user-extensible way. It graphically displays the ASCII and cbf files that XDS writes and can run useful shell commands with a simple mouse click.
an open source build of XDSGUI.
a program that allows processing of datasets in a given directory with minimum effort when you supply it with a result directory and the directory where your frames are stored. All datasets consisting of more than 100 frames within the given directory and all its subdirectories will be processed. For each dataset a space group assignment is done using POINTLESS from the CCP4 software …
a collection of python scripts made to simplify the processing of crystal diffraction images with the XDS Program Package. Provided that the diffraction parameters are well recorded in the diffraction image headers, XDS data processing can be started with a simple command lines (see manual for details).
a home-brewn program that prints various statistics (that are not available from XDS itself) in the form of tables and images.
an X-ray diffraction and control image viewing utility for data processed using the XDS program package.
a program for interactive, computer-supported NMR spectrum analysis.
Keywords:
NMR
an expert system for automated reduction of X-Ray diffraction data from macromolecular crystals, making use of existing software (CCP4, XDS, Phenix, CCTBX.) XIA2 is now included with DIALS. In SBGrid, XIA2 is provided by a few different titles. Run ``` xia2 --sbapp:l ``` to see the complete list. The most recent release can usually be found in the latest release of DIALS.
(X-Window-based Microscopy Image Processing Package) a suite of image processing programs primarily aimed at single-particle 3D electron microscopy.
a package for biomolecular structure determination from experimental NMR data combined with known geometric data. Xplor–NIH was derived from XPLOR version 3.851 and contains all of the functionality therein in addition to numerous new features designed to render a highly flexible architecture and foster the rapid and easy development of new functionality.
Keywords:
NMR
a tool that uses interactive computer graphics to introduce basic concepts of X-ray diffraction by crystals, including the reciprocal lattice, the Ewald sphere construction, Laue cones, the wavelength dependence of the reciprocal lattice, primitive and centered lattices and systematic extinctions, rotation photography, Laue photography, space group determination and Laue group symmetry, and the alignment of crystals by examination of reciprocal space.
an interactive image manipulation program for the X Window System that operates on images in the GIF, JPEG, TIFF, PBM, PGM, PPM, XPM, X11 bitmap, Sun Rasterfile, Targa, RLE, RGB, BMP, PCX, FITS, and PM formats on all known types of X displays. It can generate PostScript files, and (with ghostscript version 2.6 or above) it can also display them.
Keywords:
Other
(Yammp Under Python) a molecular modeling program designed as a general purpose tool, although development is currently concentrated on molecular simulations (mechanics) and on reduced representation and multiscale modeling. YUP is based on an earlier program Yammp. Also known as Yammp 2.
a tool for analyzing and manipulating images, especially those generated for electron microscopy. Zephyr is scriptable in Python, easy to extend, and easy to link to other programs.
a subset of chemical compounds that are used for screening at the ICCB-Longwood Screening Facility. The dataset was compiled by David Wrobel (ICCB-Longwood) for in silico docking. The date-stamped datasets are available in /programs/share/iccb.
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