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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.
an implementation of the inference pipeline of AlphaFold v2.0 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.
AMPLIFY is 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.
(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.

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 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 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.
(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.
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.
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 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.
(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.
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 tool that implements fast, high-performance, quantum mechanical and molecular mechanical algorithms in an easy-to-use approach to accelerate drug discovery and development.
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 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.
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
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.
Keywords:
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.
Keywords:
Other