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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.
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.
consists of the standalone program ALBULA VIEWER, 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.
a bioinformatics tool to generate customized fold libraries for fragment-based molecular replacement. It provides several algorithms to interpret and analyze protein structures.
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 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.
allows the user to perform interactive comparisons between RNA structures and to conduct database searches for specific RNA structures or substructures.
(Alignment of Multiple Protein Sequences) a suite of programs for protein multiple sequence alignment, pairwise alignment, statistical analysis and flexible pattern matching.
a Python distribution that includes more than 400 of the most popular Python packages for science, math, engineering, and data analysis.
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.
(Ambiguous Restraints for Iterative Assignment) a software that automates NOE assignment and NMR structure calculation.
Keywords:
NMR
aria2 is 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.
AutoDock for GPUs and other accelerators, Cuda accelerated version of AutoDock4.2.6. 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.
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
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.
(Buffalo n' Pittsburgh Interface) for complete protein phasing; combines SnB and the Phases Suite.
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
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.
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.
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 spectroscopy integrated with the CCP data model, inspired partly by the program ANSIG (Per Kraulis) and partly by the program Sparky (T.D.Goddard and D.G.Kneller, UCSF).
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
is 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.
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.
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.
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) 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.
an easy-to-use Notebook based environment for fast and convenient protein structure predictions.
a program for molecular replacement calculations, using the combined molecular replacement method.
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) 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
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.
crossflaghkl partitions a merged hkl-file into k subsets with the number of reflections marked with -1.
an automatic pipeline for cryo-EM data preprocessing and assessment using a combination of deep learning and image analysis tools.
PIP package memory efficient implementation of cryoCARE (Content-Aware Image Restoration for Cryo-Transmission Electron Microscopy Data), is a restoration method that dramatically increases contrast in cryo-TEM images, improving the interpretability of the acquired 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.
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.
(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
CTFFIND3 and CTFTILT are two programs for finding CTFs of electron micrographs.
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.
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
(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/
is 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 suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. deepTools contains useful modules to process the mapped reads data for multiple quality checks, creating normalized coverage files in standard bedGraph and bigWig file formats, that allow comparison between different files (for example, treatment and control). Finally, using such normalized and standardized files, …
(Dynamics Extraction From cryo-em Map) provides 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.
(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.
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.
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 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 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) is a GUI to allow the general user to run DIALS tools and inspect the output without resorting to detailed command-line usage.
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 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.
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.
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).
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.
(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 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.
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 to predict protein structure, function, and mutations using evolutionary sequence covariation.
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
FDT is 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
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
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.
enables fast and sensitive comparisons of large structure sets.
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.
(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.
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 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
combined 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.
Keywords:
Other
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 models.
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.
Keywords:
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.
Keywords:
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
Keywords:
Other
a versatile package that performs molecular dynamics of proteins, lipids and nucleic acids.
Protein-ligand docking programs are indispensable tools for predicting the binding pose of a ligand to the receptor protein. 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.
Keywords:
Other
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 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
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.
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.
Keywords:
Other
Illustrate is 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 …
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.
Keywords:
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.
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) designed to allow mixing and matching of existing modeling components as well as the easy addition of new functionality.
(INFERence of RNA ALignment) 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.