All Software

SBGrid supports 283 structural biology software titles. The following software packages are supported by SBGrid; availability of a specific software package may be limited based on license requirements.

Software Title Description Linux 32-bit Linux 64-bit OS X Intel Links

2dx

- a package for data processing of 2DX crystals developed by the Stahlberg laboratory at the University of Basel.

yes yes yes

3DNA

- a package for analyzing, visualizing and rebuilding 3-dimensional nucleic acid structures. 3DNA was created by Dr. Xiang-Jun Lu in the laboratory of Professor Wilma K. Olson at the Department of Chemistry and Chemical Biology, Rutgers-the State University of New Jersey.

yes yes yes

a2ps

- an Any-to-PostScript filter. It processes plain text files, but also pretty prints quite a few popular languages.

yes yes yes

ACE2

A CTF Estimator (ACE) 2. 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 in written in objective C, it no longer requires MATLAB to work.

yes yes yes

ACEMD

ACEMD is heavily optimized molecular dynamics (MD) engine specially designed to run on NVIDA GPUs. ACEMD is extremely fast (115ns/day for DHFR using 1 GPU) and allows performing MD simulations on the microsecond scale in a single workstation. ACEMD is a fully featured platform (PME, NPT, NVT, TCL, PLUMED, CAMSHIFT), that can read CHARMM/NAMD and AMBER input files. Furthermore, ACEMD works with CUDA and OpenCL and uses similar syntax to other MD software. ACEMD has been validated by numerous studies and powers GPUGrid, one of the largest distributed computing projects worldwide. Parallel, fully supported versions of ACEMD are available through Acellera.

yes

adxv

- 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. adxv was written by Andrew Arvai.

yes yes yes

Aline

- 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. Developed by Charlie Bond and Alex Schüttelkopf.

yes yes yes

Alscript

- 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.

yes yes

AmberTools

AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB), with generalized Born solvent models

yes yes yes

AMIGOS II

- allows the user to perform interactive comparisons between RNA structures and to conduct database searches for specific RNA structures or substructures. AMIGOS II was authored by Leven Wadley in the lab of Anna Marie Pyle at Yale University.

yes yes yes

AMPS

- a suite of programs designed for the alignment of multiple protein sequences and flexible pattern matching.

yes yes yes

APBS

- a software package designed for the numerical solution of the Poisson-Boltzmann equation (PBE). This software was written by Nathan Baker in collaboration with J. Andrew McCammon and Michael Holst and enhanced by several others.

yes yes yes

Appion

Appion is a "pipeline" for processing and analysis of EM images. Appion is integrated with "Leginon":http//leginon.org data acquisition but can also be used stand-alone after uploading images (either digital or scanned micrographs) or particle stacks using a set of provided tools. Appion consists of a web based user interface linked to a set of python scripts that control several underlying integrated processing packages. All data input and output within Appion is managed using tightly integrated SQL databases. The goal is to have all control of the processing pipeline managed from a web based user interface and all output from the processing presented using web based viewing tools.

yes yes

AQUA

- a suite of programs that analyze the quality of biomolecular structures determined via NMR spectroscopy. AQUA was initially developed by Ton Rullmann and Jurgen Doreleijersb Bijvoet Center for Biomolecular Research, Utrecht, The Netherlands. Current maintenance and expansion by Jurgen Doreleijers, BioMagResBank, University of Wisconsin-Madison, USA.

yes yes yes

ARIA

- (Ambiguous Restraints for Iterative Assignment) is a software that automates NOE assignment and NMR structure calculation. ARIA was originally developed in Michael Nilges's team at the European Molecular Biology Laboratory, Heidelber by François-Regis Chalaoux, Dinu Gherman, Jens Linge, Michael Nilges and Sean O'Donoghue. Since 2001, BIS (Bioinformatique Structurale) team, and specifically Michael Habeck and Wolfgang Rieping, Institut Pasteur, in Paris.

yes yes yes

ARP/wARP

An interpretation of crystallographic electron density maps and automatic construction and refinement of macromolecular models. At the request of the developer, this software is licensed on a per-user basis. To obtain an ARP/wARP license and enable use in the SBGrid environment, each user should: - visit the [ARP/wARP website](http://www.embl-hamburg.de/ARP/) to request a license. - download any of the current versions via your web browser. - in the shell run 'sbgrid-register -r path/to/the/arp_warp-file-you-downloaded'. - open a new terminal to utilize the newly registered software title. Please cite the applications of ARP/ wARP that you have used. Please consult the ARP/ wARP log file for the most relevant citation. The complete citation list is in the [ARP/wARP manual][arpman] . [arpman]:http://www.embl-hamburg.de/ARP/Manual/UserGuide7.4.html#x1-530005

yes yes yes

ATSAS

- a program suite for small-angle scattering (SAXS) data analysis from biological macromolecules. <br><br> ATSAS is freely available to non-profit labs, but each lab must register with EMBL before we can install the software. To include this software in your installation, please register here <a href = "http://www.embl-hamburg.de/biosaxs/atsas-online/register.php">http://www.embl-hamburg.de/biosaxs/atsas-online/register.php</a>, then send a copy of your registration confirmation to us at <a href = "mailto:licensing@sbgrid.org">licensing@sbgrid.org</a>. <br><br> This suite of programs was developed in Dmitri Svergun's group at EMBL Hamburg. Authorship by program is as follows: PRIMUS - P.V. Konarev, A.G. Kikhney, A.V. Sokolova, D.I. Svergun & V.V. Volkov GNOM - D.I. Svergun & A. Semenyuk DAMMIN - D.I. Svergun with M. Kozin, M. Petoukhov, V. Volkov DAMMIF - D. Franke MONSA, GASBOR, SASREF, BUNCH, CORAL, GLOBSYMM, DAMAVER - M.V. Petoukhov & D.I. Svergun MASSHA - P.V. Konarev, M.V. Petoukhov, D.I. Svergun & V.V. Volkov OLIGOMER - D.I. Svergun with A.V. Sokolova, P.V. Konarev, V.V. Volkov MIXTURE - P.V. Konarev, D.I. Svergun1 & V.V. Volkov EOM - P. Bernadó, E. Mylonas, M.V. Petoukhov & D.I. Svergun CRYSOL - D. Svergun, C. Barberato, M. Malfois, V. Volkov, P. Konarev, M. Petoukhov & A. Shkumatov CRYSON - D. Svergun, M. Malfois, M. Petoukhov & A. Shkumatov SUPCOMB - M.B. Kozin, M.V. Petoukhov & D.I. Svergun DARA - A. V. Sokolova, V. V. Volkov & D. I. Svergun SASHA - D.I. Svergun & V.V. Volkov ASSA - M.B. Kozin & D.I. Svergun CREDO - M.V. Petoukhov & D.I. Svergun

yes yes yes

AUTO3DEM

- 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).

yes yes yes

AutoDock

- a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of a known 3D structure.

yes yes yes

AutoDock Vina

- an open-source program for drug discovery, molecular docking, and virtual screening, offering multi-core capability, high performance and enhanced accuracy and ease of use.

yes yes yes

autoPROC

autoPROC combines third-party processing programs with new tools and an automated workflow script for automated treatment of multi-sweep X-ray diffraction data. <br><br> autoPROC is freely available to academic labs, but each lab must register with Global Phasing before this software can be used. To include this software in your installation, please submit a license request to <a href = "http://www.globalphasing.com/autoproc/licence/request.html">http://www.globalphasing.com/autoproc/licence/request.html</a>, then copy your license file to /programs/local/autoproc/autoproc_licence, and the software will start working.

yes yes

Avogadro

Avogadro is 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.

yes yes yes

BALBES

- 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.

yes yes yes

BEST

- a program for optimal planning of X-ray data collection from protein crystals. <br><br> BEST is freely available to non-profit labs, but each lab must register with EMBL before we can install the software. To include this software in your installation, please register here <a href = "http://www.embl-hamburg.de/BEST/download_request3.1.html">http://www.embl-hamburg.de/BEST/download_request3.1.html</a>, then send a copy of your registration confirmation to us at <a href = "mailto:licensing@sbgrid.org">licensing@sbgrid.org</a>. <br><br>

yes yes yes

bfactor

bfactor is a program for filtering 3D maps and applying B-factors.

yes yes yes

BioPerl

- a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.

yes yes yes

BioPython

- a set of tools for biological computation written in Python by an international team of developers.

yes yes yes

BLAST

- (Basic Local Alignment Search Tool) finds regions of similarity between biological sequences.

yes yes yes

BLAST+

- (Basic Local Alignment Search Tool) finds regions of similarity between biological sequences.

yes yes yes

BnP

- Buffalo and Pittsburgh) an interface for complete protein phasing suite includes SnB and Phases.

yes yes

BOBSCRIPT

- an extension to Molscript

yes yes yes

breseq

- a computational pipeline for finding mutations relative to a reference sequence in short-read DNA.

yes yes yes

Bsoft

- a software package written for image processing of electron micrographs, interpretation of reconstructions, molecular modeling, and general image processing.

yes yes yes

Burnham-Brandeis Helical Package

- a suite of applications for the analysis of helical structures.

yes yes yes

BUSTER

BUSTER is a software system for crystallographic structure determination by Bayesian statistical methods <br><br> BUSTER is freely available to academic labs, but each lab must register with Global Phasing before this software can be used. To enable this software in your installation, please submit a license request to <a href = "http://www.globalphasing.com/autoproc/licence/request.html">http://www.globalphasing.com/autoproc/licence/request.html</a>, then copy your license file to /programs/local/buster/buster_licence, and the software will start working.

yes

CARA

- an application for the analysis of NMR spectra and compute- aided resonance assignment.

yes yes yes

CAVER

CAVER is a software tool for analysis and visualisation of tunnels and channels in protein structures. Tunnels are void pathways leading from a cavity buried in a protein core to the surrounding solvent. Unlike tunnels, channels lead through the protein structure and their both endings are opened to the surrounding solvent. Studying of these pathways is highly important for drug design and molecular enzymology. This is the command line version and not the PyMOL plugin version.

yes yes yes

CCP4

- (Collaborative Computational Project, Number 4) a collection of programs and associated data and software libraries which can be used for macromolecular structure determination by X-ray crystallography. <br><br> CCP4 is freely available to non-profit labs, but each lab must complete the CCP4 <a href= "http://www.ccp4.ac.uk/ccp4license.php">license</a> and return the executed document directly to the STFC Daresbury Laboratory, as specified on the CCP4 webpage.

yes yes yes

CCP4mg

- offers a quick and easy way to create beautiful publication quality images and movies and to superpose and analyze structures.

yes yes yes

CcpNmr

- an analysis program built on top of 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).

yes yes yes

CcpNmr ChemBuild

CcpNmr ChemBuild is a graphical tool to construct chemical compound definitions for NMR. While there are many chemical structure drawing packages available ChemBuild was especially created to handle concepts like protonation variants and magnetic equivalence which 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.

yes yes yes

Chimera

- a highly extensible, interactive molecular graphics program, often a tool of choice for rendering EM volumes.

yes yes yes

Clustal

- a general purpose multiple sequence alignment program for DNA or proteins.

yes yes yes

CMView

- an interactive contact map visualization and analysis tool that supports assessing similarities and differences between structure- or contact predictions.

yes yes yes

CNS

- an X-ray crystallography suite used for refinement, phasing, and molecular replacement

yes yes yes

COMO

- is a program for molecular replacement calculations, using the combined molecular replacement method.

yes yes yes

CONCOORD

- a method to generate protein conformations around a known structure based on geometric restrictions.

yes yes yes

Coot

- (Crystallographic Object-Oriented Toolkit) supports model building and real space refinement. The application interfaces with refmac, Phenix, and several other applications. Coot was recognized as the best structural biology application in 2008 by SBGrid.

yes yes yes

CPMGFit

- a program for non-linear least squares fitting of CPMG relaxation dispersion curves.

yes yes yes

crop

crop is a program for cutting sections out of 2D and 3D density maps.

yes yes yes

CrystFEL

CrystFEL is 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.

yes yes

CS-ROSETTA

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. This software is computationally intensive and would ideally be run on a cluster. The University of Wisconsin hosts a [web front end for CS-Rosetta][1] that runs jobs on the Open Science Grid (100k+ CPUs) and is free for academic users. [1]: https://condor.bmrb.wisc.edu/rosetta/

yes yes yes

CTF

CTFFIND3 and CTFTILT are two programs for finding CTFs of electron micrographs [1]. The program CTFFIND3 is an updated version of the program CTFFIND2, which was developed in 1998 by Nikolaus Grigorieff at the MRC Laboratory of Molecular Biology in Cambridge, UK with financial support from the MRC.

yes yes yes

Curves+

- a complete rewrite of the Curves approach for analyzing the structure of nucleic acids. Included are the helper programs Canal, Cdif and Sumr.

yes yes yes

CURVES

- an algorithm for calculating a helical parameter description for any irregular nucleic acid segment with respect to an optimal, global helical axis.

yes yes yes

CYANA

- a program for the automated structure calculation of biological macromolecules on the basis of conformational constraints from NMR. <br><br> CYANA is a commercial software application that we can include in your installation for ease of use, but that requires you or your institute to have a current license in place. To enable the SBGrid installation for CYANA please send an email to <a href = "mailto:licensing@sbrid.org">licensing@sbgrid.org</a> with information confirming that your license is active. <br><br>

yes yes yes

DelPhi

A program for calculating protein electrostatics. <br><br> DelPhi is freely available to non-profit labs, but each lab must register with Columbia before we can install the software. To include this software in your installation, please register here <a href = "https://bhapp.c2b2.columbia.edu/software/cgi-bin/software.pl?input=DelPhi">https://bhapp.c2b2.columbia.edu/software/cgi-bin/software.pl?input=DelPhi</a>, then send a copy of your registration confirmation to us at <a href = "mailto:licensing@sbgrid.org">licensing@sbgrid.org</a>. <br><br>

yes yes yes

Desmond

is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems on conventional commodity clusters. The code uses novel parallel algorithms and numerical techniques to achieve high performance and accuracy on platforms containing a large number of processors, but may also be executed on a single computer.

diffmap

diffmap is 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.

yes yes yes

DINO

- a realtime 3D visualization program for structural biology data.

yes yes yes

DOCK

- a molecular docking application that can be used to a) predict binding modes of small molecule-protein complexes; b)search databases of ligands for compounds that inhibit enzyme activity; c) search databases of ligands for compounds that bind a particular protein; d) search databases of ligands for compounds that bind nucleic acid targets; e) examine possible binding orientations of protein-protein and protein-DNA complexes; f) help guide synthetic efforts by examining small molecules that are computationally derivatized. A recent publication (see citations) describes how DOCK can be used to model RNA--small molecule complexes.

yes yes yes

Dowser

- a program that surveys a protein molecule's structure to locate internal cavities and assess the hydrophilicity of those cavities 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.

yes yes yes

DPS

- (Data Processing Suite) a suite of programs for processing of 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. The software website has not been updated since 2000, but software updates are posted on a regular basis.

yes yes

DSSP

- 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

yes yes yes

DSSR

A software program for Defining the Secondary Structures of RNA from three-dimensional coordinates.

yes yes

d*TREK

- a software suite and toolkit that processes single crystal X-ray diffraction images from two-dimensional position sensitive detectors. <br><br> d*TREK is a commercial software application that we can include in your installation for ease of use, but that requires you or your institute to have a current license in place. To enable the SBGrid installation for d*TREK please send an email to <a href = "mailto:licensing@sbrid.org">licensing@sbgrid.org</a> with information confirming that your license is active. <br><br>

yes yes yes

Dynamo

Dynamo is a software environment for subtomogram averaging of cryo-EM data. Our goal is to provide a reliable tool for all kind of users: newcomers needing a mild learning curve, advanced users with lots of data to process as fast as possible, and developers that need a flexible framework to test new ideas and algorithms.

yes yes

DynDom

- a program to determine domains, hinge axes and hinge bending residues in proteins where two conformations are available.

yes yes yes

DynDom3D

- a new program to analyze domain movements in large, multi-chain, biomolecular complexes. This program is applicable to any molecule for which two atomic structures are available that represent a conformational change indicating a possible domain movement. Unlike the original DynDom (DynDom1D), this method is blind to atomic bonding and atom type and can, therefore, be applied to biomolecular complexes containing different constituent molecules such as protein, RNA or DNA.

yes yes yes

Eden

- a crystallographic real-space electron-density refinement and optimization program that produces electron density maps with minimal model bias in a robust manner.

yes yes yes

Electra

- (ELECtron Tomography Resolution Assessment) a suite of programs written to estimate the resolution of electron density volumes obtained by electron tomography.

yes yes yes

Elves

- 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.

yes yes yes

em2em

- a program to convert images from/to formats used in the "electron microscopical community" (3DEM)

yes yes yes

EMAN

- a suite of scientific image processing tools for the transmission electron microscopy community, though it is beginning to be used in other fields as well. EMAN has a particular focus on single particle reconstruction. EMAN includes Foldhunter and Helixhunter.

yes yes yes

EMAN2

- 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. The new system offers an easily extensible infrastructure, better documentation, easier customization, etc. However, it will be some time before the full capabilities of EMAN1 have been reimplemented in the new system. For this reason EMAN2 was designed to happily coexist with EMAN1 installations. It is strongly recommended that all EMAN2 installations be accompanied by an EMAN1 installation. The programs that DO exist in EMAN2 will generally be more capable and efficient than the EMAN1 counterparts.

yes yes yes

EM-BFACTOR

- 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). The program accepts 3D maps in any common EM format and also accepts FSC curves in the format of most common packages for single particles, cryoEM. As output, the program produces a sharpened map and the Guinier plot that allows assessment of the sharpening.

yes yes yes

EMBOSS

- integrates a range of currently available packages and tools for sequence analysis into a seamless whole.

yes yes yes

EM Imaging Processing GUI (EMIP)

- (EM Imaging Processing GUI) is a Graphical User Interface written in wxPython that collects information from the user and runs existing programs from a variety of different software packages.

yes yes yes

ENTANGLE

- 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. These interactions are then classified into hydrogen bonds, electrostatic, hydrophobic, and Van der Waals. Entangle also recognizes when a stacking interaction occurs between two aromatic residues. In addition to a listing, Entangle allows the user to probe the interface in three-dimensions.

yes yes yes

EPMR

- 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.

yes yes yes

ESCET

- 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. <br><br> ESCET is freely available to non-profit labs, but each lab must register with EMBL before we can install the software. To include this software in your installation, please register here <a href = "http://www-db.embl.de/jss/EmblGroupsOrg/mail_1.html?addressName=pers_4572&designID=121">http://www-db.embl.de/jss/EmblGroupsOrg/mail_1.html?addressName=pers_4572&designID=121</a>, then send a copy of your registration confirmation to us at <a href = "mailto:licensing@sbgrid.org">licensing@sbgrid.org</a>. <br><br>

yes yes

ESPript

- (Easy Sequencing in Postscript) is a utility to generate a pretty PostScript output from aligned sequences and coordinate files.

yes yes yes

FASTA

- a DNA and protein sequence alignment software package that searches for matching sequence patterns or words, called k-tuples. Its legacy is the FASTA format which is now ubiquitous in bioinformatics. First described (as FASTP) by David J. Lipman and William R. Pearson in 1985.

yes yes yes

FAST ModelFree

FASTModelFree is 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.

yes yes yes

Fiji

Fiji is an image processing package. It can be described as a distribution of ImageJ (and soon 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. The main focus of Fiji is to assist research in life sciences.

yes yes yes

FinchTV

FinchTV is the 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.

yes yes yes

fpocket

fpocket is a very fast 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.

yes yes yes

FREALIGN

- (Fourier REconstruction and ALIGNment) a program for high-resolution refinement of 3D reconstructions from cryo-EM images of single particles. A GPU-enabled version is also available. Developed by Niko Grigorieff at Brandeis University.

yes yes yes

Gamma

This software is a package of C++ libraries that allow simulation of NMR experiments. It is used for designing and analysing NMR pulse sequences.

yes yes yes

GeFREALIGN

FREALIGN is a program developed by Niko Grigorieff laboratory for high-resolution refinement of 3D reconstruction from cryoEM of single particles. GeFREALIGN is a version modified to run on GPU processors so that the refinement process of single particle 3D reconstruction can be speedup. All the algorithms from the original FREALIGN are kept unchanged. For detailed description of original FREALIGN, please refer to the FREALIGN website. The current GPU-enabled FREALIGN was written by Xueming Li at Yifan Cheng laboratory, UCSF. Same as the original FRELIGN, the GPU-enabled FREALIGN is available for download and licensed under the terms of the GNU Public License version 3 (GPLv3).

yes

Geneious

Beautiful sequence alignment, assembly and analysis software. We currently have a temporary license for up to 250 concurrent users with plans for a permanent 10 seat license in the future provided that number meets current needs.

yes yes

Ghostscript

- an interpreter for the PostScript (TM) language. It can display and convert postscript files. Software can be involved with gs command.

yes yes yes

Gnuplot

- 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.

yes yes yes

Gorgon

Gorgon is 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.

yes yes yes

Grace

- a general plotting, curve fitting and data trasformation program.

yes yes yes

Graphviz

- an open-source graph visualization software program. A gallery of images is available on the developer's website: http://www.graphviz.org/Gallery.php

yes yes yes

Grigorieff Apps

- EM utilities from the lab of Niko Grigorieff that include ctffind, ctftilt, bfactor, crop, diffmap and rmeasure.

yes yes yes

GROMACS

- a versatile package that performs molecular dynamics of proteins, lipids and nucleic acids. GROMACS was first developed in Herman Berendsens group, department of Biophysical Chemistry of Groningen University. It is a team effort, which is currently lead by Erik Lindahl, David van der Spoel and Berk Hess. GROMACS offers a user friendly interface and provides high performance.

yes yes yes

HADDOCK

- (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. HADDOCK was written by Alexandre Bondvin is derived from ARIA scripts by Michael Nilges and Jens Linge.

yes yes yes

HBPLUS

- a program suite (hbplus, access and clean) to compute hydrogen positions, hydrogen bonds, and neighboring interactions. The application was developed at University College London.

yes yes yes

HKL2000

- 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). <br><br> HKL2000 is a commercial software application that we can include in your installation for ease of use, but that requires you or your institute to have a current license in place. To enable the SBGrid installation for HKL2000, copy the license file to the directory /usr/local/lib on each machine and HKL2000 will work.

yes yes yes

HKL2MAP

A graphical user-interface for macromolecular phasing. HKL2MAP is freely available to non-profit labs, but each lab must register with EMBL before we can install the software. To include this software in your installation, please register [here][1], then send a copy of your registration confirmation to us at <licensing@sbgrid.org>. [1]: http://webapps.embl-hamburg.de/bundle/download.php?hkl2mp=true&sitcom=false

yes yes yes

HOLE

- a program that allows the analysis and visualisation of the pore dimensions of the holes through molecular structures of ion channels. The application was developed by Oliver S. Smart, and is currently hosted by the Sansom Laboratory at the University of Oxford.

yes yes yes

HYDRONMR

HYDRONMR is a computer 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 coordintes. For this purpose, the basic hydrodynamic quantities that are involved in dynamic NMR are evaluated in the same fashion as in the closely related HYDROPRO program. Then, HYDRONMR calculates NMR quantities like T1, T2, NOE, etc. for each residue of a globular protein (the 15N-H and 13Ca -H vectors are calculated by the program itself. Alternatively, an user-supplied list of vectors can be given. HYDRONMR also reports the translational diffusion coefficient, which is available, among other sources, from some NMR experiments.

yes yes

HYDROPRO

HYDROPRO 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. The HYDROPRO calculation comprises the basic hydrodynamic properties: translational diffusion coefficient, sedimentation coefficient, intrinsic viscosity, and relaxation times, along with the radius of gyration.

yes yes

ilastik

- a simple, user-friendly tool for image classification and segmentation in up to three spatial and one spectral dimension. Using it requires no experience in image processing. ilastik has a convenient mouse interface for labeling an arbitrary number of classes in the images. These labels, along with a set of generic (nonlinear) image features, are then used to train a Random Forest classifier. In the interactive training mode, ilastik provides real-time feedback of the current classifier predictions and thus allows for targeted training and overall reduced labeling time. In addition, an uncertainty measure can guide the user to ambiguous regions of the data. Once the classifier has been trained on a representative subset of the data, it can be exported and used to automatically process a very large number of images. The features are computed in the full 2D/3D/4D pixel neighborhoods, depending on the available data. While the provided set of features includes popular color, edge and texture descriptors, the plug-in functionality allows advanced users to add their own problem-specific features. Feature computation and classifier prediction are multi-threaded and fully exploit modern multi-core machines.

yes yes

ImageJ

ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh. It 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". It supports "stacks", a series of images that share a single window. It is multithreaded, so time-consuming operations such as image file reading can be performed in parallel with other operations. This installation includes the LOCI BioFormats plugin for reading and editing EM image stacks.

yes yes yes

ImageMagick

- a software suite to create, edit, compose, or convert bitmap images.

yes yes yes

IMOD

- a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial- and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and displaying the image files. IMOD was developed primarily by David Mastronarde, Rick Gaudette, Sue Held, Jim Kremer, and Quanren Xiong at the Boulder Laboratory for 3-D Electron Microscopy of Cells.

yes yes yes

iMosflm

- a data processing application for macromolecular crystallography. iMosflm (Graphical User Interface) and Mosflm (data processing application) are distributed with this package. iMosflm is maintained by Harry Powell and distributed under a CCP4 license.

yes yes yes

Integrative Modeling Platform (IMP)

- is designed to allow mixing and matching of existing modeling components as well as the easy addition of new functionality.

yes yes yes

istHMS

istHMS was developed at Harvard Medical School as an algorithm to reconstruct non-uniformly acquired NMR data.

yes yes yes

Jalview

- 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.

yes yes yes

LAFIRE

- (Local-correlation-coefficient-based Automatic FItting for REfinement) is 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.

yes yes yes

LigPlot+

- a graphical front-end to the LIGPLOT (protein-ligand interactions) and DIMPLOT (protein-protein, domain-domain interactions) programs. The plots generated by these programs can be interactively edited on screen, superposed and printed.

yes yes yes

LIGPLOT

- a program for automatically plotting protein-ligand interactions.

yes yes yes

MadBend

- 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 thus describe the direction and magnitude of a bend angle and can be used to analyze DNA and DNA/protein complex geometries.

yes yes

MAFFT

- a multiple sequence alignment program. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼10,000 sequences), etc.

yes yes yes

MAIN

- a model building application for X-ray crystallography.

yes yes yes

MAMMOTH-Mult

- 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.

yes yes yes

Matt

- 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.

yes yes yes

Maxit

- was developed by the PDB (Protein Data Bank) and NDB (Nucleic Acid Database) to assist in the processing and curation of macromolecular structure data. Features include reading and writing PDB and mmCIF format files, and translating between file formats.

yes yes yes

MCCE

- Multi-Conformation Continuum Electrostatics) is 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.

yes yes yes

Mead

- 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.

yes yes yes

MES

- (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.

yes yes yes

MGLTools

- a software package comprised of AutoDockTools (adt), Python Molecule Viewer (pmv) and a python programming environment called Vision. Developed at the Molecular Graphics Laboratory (MGL) of The Scripps Research Institute for visualization and analysis of molecular structures. <p> AutoDockTools is graphical front-end for setting up and running AutoDock - an automated docking software designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. <p> PMV is a powerful molecular viewer that has a number of customizable features and comes with many pluggable commands ranging from displaying molecular surfaces to advanced volume rendering. <p> Vision is a visual-programming environment in which a user can interactively build networks describing novel combinations of computational methods, and yielding new visualizations of their data without actually writing code.

yes yes yes

MIExpert

- an expert system for running molecular replacement and refinement applications, and analyzing the data obtained from high-throughput co-crystallography and fragment screening projects. MIExpert is a module of MIFit.

yes

MIFit

- 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.

yes yes

MMC

MMC is a Metropolis Monte Carlo 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).

yes yes

MMTSB Toolset

Multiscale Modeling Tools for Structural Biology

yes yes yes

ModelFree

- 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.

yes yes yes

MODELLER

- is used for homology or comparative modeling of protein three-dimensional structures. The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints, and can perform many additional tasks, including de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc. A graphical interface to MODELLER is commercially available from Accelrys, as part of Discovery Studio Modeling 1.1.

yes yes yes

MODULE

- 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.

yes yes yes

MOLE

- a universal toolkit for rapid and fully 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. MOLE is a powerful software program for exploring large molecular channels, complex networks of channels and molecular dynamics trajectories in which analysis of a large number of snapshots is required.

yes yes yes

MOLMOL

- a molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules.

yes yes yes

MOLPHY

- (MOLecular PHYlogenetics) is a computer program package for molecular phylogenetics.

yes yes yes

MolScript

MolScript is one of the most popular programs for the generation of publication-quality figures.

yes yes yes

MOSFLM

- a package for processing film and image plate data.

yes yes yes

MRC Cambridge Image Processing System

- 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.

yes yes yes

mrtailor

mrtailor - PDB preparation tool for use with ProSmart or for Molecular Replacement

yes yes yes

MUSCLE

- (multiple sequence comparison by log-expectation) is a public domain multiple alignment software for protein and nucleotide sequences.

yes yes yes

NACCESS

- a stand-alone program that calculates the accessible area of a molecule from a PDB format file.

yes yes yes

NAMD

- a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

yes yes yes

NEdit

- 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.

yes yes yes

Nessy

NESSY is 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.

yes yes yes

NETBLAST

- NETBLAST is 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).

yes yes yes

NMRPipe

- 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.

yes yes yes

NMRVIEW

- is used to visualize and Analyze Nuclear Magnetic Resonance Data.

yes yes yes

NORMA

- 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. A typical application for this software is the interpretation of electron microscopy data using atomic scale resolution structural models. The software package provided here should enable the interested user to perform flexible fitting on new cases without encountering major technical difficulties.

yes yes

NUCCYL

- a Perl program that allows PyMOL to display atomic models of nucleic acids in a highly simplified representation.

yes yes yes

NUCPLOT

- 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.

yes yes yes

O

- a model building application for X-ray crystallography.

yes yes yes

OpenBabel

- 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.

yes yes yes

PARTICLE

PARTICLE is 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.

yes yes

PDB2PQR

PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a platform-independent utility for converting protein files in PDB format to PQR format. These tasks include: - Adding a limited number of missing heavy atoms to biomolecular structures - Determining side-chain pKas - Placing missing hydrogens - Optimizing the protein for favorable hydrogen bonding - Assigning charge and radius parameters from a variety of force fields

yes yes yes

pdb-care

The pdb-care program is able to identify and assign 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. Additionally, the reliability of reported and calculated connectivities for molecules listed within the HETATOM records is checked and unusual values are reported.

yes

PDB_REDO

PDB_REDO 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.

yes

PDB Validation Suite

- a set of tools used by the PDB for processing and checking structure data.

yes yes yes

Perl

The Pathologically Eclectic Rubbish Lister, sometimes also called the Practical Extraction and Reporting Language.

yes yes yes

PFT3dr

- performs orientation searches and positional refinement of icosahedral viruses.

yes yes yes

PGPLOT

- a Fortran- or C-callable, device-independent graphics package for making simple scientific graphs.

yes yes yes

PHASES

- computes phase angles for diffraction data from macromolecular crystals. The package contains 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 (multiple isomorphous replacement), SIR (single isomorphous replacement), SAS (single wavelength anomalous scattering), SIRAS (single isomorphous replacement supplemented with anomalous scattering), MIRAS (multiple isomorphous replacement supplemented with anomalous scattering) or from atomic coordinates for an input model; noncrystallographic symmetry averaging; combining phases from a partial structure with MIR etc phases; computation and analysis of cross difference or Bijvoet difference Fourier maps; and for phase extension and refinement.

yes yes yes

PHENIX

- (Python-based Hierarchical Environment for INtegrated Xtallography) provides tools for automated structure solution by X-ray crystallography. The PHENIX software provides algorithms to proceed from reduced intensity data to a refined molecular model, and facilitate structure solution for both the novice and expert crystallographer. We also maintain a recent PHENIX nightly build in the software suite.

yes yes yes

PHOELIX

- a software package for image processing of helical macromolecular complexes.

yes yes yes

PHYLIP

- a free package of software programs for inferring phylogenies.

yes yes yes

pipe2xeasy

- performs conversions of spectra from NMRPipe to XEASY format. pipe2xeasy can read the ASCII file with header information, which is produced with "showhdr -verb filename".

yes yes yes

PLOTMTV

PLOTMTV is a multipurpose X11 plotting program and specializes in contour plots, but it 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. The program has an rough but functional Graphical User Interface, through which it is possible to zoom in, zoom out, pan, toggle between 2D and 3D plots, and rotate 3D plots. Both color and grayscale postscript output are supported.

yes yes yes

plotutils

- 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. libplot is device-independent in the sense that its API (application programming interface) does not depend on the type of graphics file to be exported. Besides libplot, the package contains command-line programs for plotting scientific data. Many of them use libplot to export graphics.

yes yes yes

POVRAY

- (Persistence of Vision Raytracer) is 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.

yes yes yes

Prediction of ALignmEnt from Structure (PALES)

- a software for the analysis of residual dipolar couplings. Its main component is the PALES (Prediction of ALignmEnt from Structure) simulation that predicts the magnitude and orientation of a sterically induced alignment tensor from a solute's (protein/nucleic acid/oligosaccharide) three-dimensional shape.

yes yes yes

Priism/IVE

- the 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.

yes yes yes

Primer3

- a widely used program that designs PCR primers (PCR = "Polymerase Chain Reaction"). Primer3 can also design hybridization probes and sequencing primers.

yes yes yes

PROBCONS

- an efficient protein multiple sequence alignment program, which has demonstrated a statistically significant improvement in accuracy compared to several leading alignment tools.

yes yes yes

Probe

- 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.

yes yes yes

PROCHECK

- checks the stereochemical quality of a protein structure, producing a number of PostScript plots analyzing its overall and residue-by-residue geometry.

yes yes yes

ProFit

- the ultimate protein least squares fitting program.

yes yes yes

PROFphd

- a new package added as part of the pipeline to create fragments for Rosetta. For commercial users, Biosof LLC (www.bio-sof.com) offers additional customization and data analysis of PROFphd.

yes yes yes

PROMALS

PROMALS (PROfile Multiple Alignment with predicted Local Structure) is a progressive method for aligning multiple protein sequences, with enhanced profile information from database searches and secondary structure prediction.

yes yes yes

PROSPECT

- a threading-based protein structure prediction system.

yes yes

Protomo

- includes programs and shell scripts for electron tomography of thin specimens. Protomo provides an interactive graphical tool for a fast initial alignment of a tilt series and shell scripts for the more time consuming refinement, as well as some other useful image manipulation utilities. The package was originally developed for the reconstruction of thin sections of insect flight muscle. More recently, it has also been successfully applied in cryo-electron tomography.

yes yes

ProtSkin

- 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 as InsightII (accelrys).

yes yes yes

PSIPRED

- uses a simple and accurate secondary structure prediction method incorporating two feed-forward neural networks which perform an analysis on output obtained from BLAST.

yes yes yes

PyMOL

- widely used molecular visualization package developed by Warren DeLano, and now maintained by Schödinger, LLC. SBGrid non-profit laboratories have full access to the official incentive builds of PyMOL. The SBGrid Consortium PyMOL license credentials are contained in the NOTES file in the PyMOL installation directories in your software installation.

yes yes yes

PyRosetta

- an interactive Python-based interface to the powerful Rosetta molecular modeling suite. It enables users to design their own custom molecular modeling algorithms using Rosetta sampling methods and energy functions.

yes yes yes

Python

- a programming language that lets you work more quickly and integrate your systems more effectively. You can learn to use Python and see almost immediate gains in productivity and lower maintenance costs. Several versions are included to support various applications.

yes yes yes

Python Macromolecular Library

is a software toolkit and library of routines for the analysis and manipulation of macromolecular structural models, implemented in the Python programming language.

yes yes

PyTOM

Cryo-electron tomography (CET) is a three-dimensional imaging technique for structural studies of macromolecules under close-to-native conditions. In-depth analysis of macromolecule populations depicted in a tomograms requires identification of subtomograms corresponding to putative particles, averaging of subtomograms to enhance their signal, and classification to capture the structural variations among them. Here, we introduce the open-source platform PyTom 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. Furthermore, we present a novel stochastic classification method that yields significantly more accurate classification results than two deterministic approaches in simulations. Finally, we demonstrate that the PyTom workflow yields faithful results for the analysis of 60S ribosomes in yeast cell lysate.

yes yes yes

Qnifft

- software for macromolecular electrostatics.

yes yes yes

QPack

- a "quick" evaluation of steric packing in protein structures. Amino acid side chains are not represented in full atomic detail. Instead, one or more averaged centers of interaction per residue are used. A measure of the quality of side chain packing is determined from the available spherical space available to each residue. Additionally, an empirical pairwise residue contact potential can be used to estimate the correctness of model protein structures.

yes yes yes

QUILT

- detects contiguous stretches of hydrophobic surface area on the surfaces of macromolecules.

yes yes yes

R

- a free software environment for statistical computing and graphics.

yes yes yes

R2R

R2R is 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.

yes yes yes

Rasmol

- 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.

yes yes yes

Raster3D

- a set of tools for generating high quality raster images of proteins or other molecules.

yes yes yes

RAW

BioXTAS RAW is a program for analysis of Small Angle X-ray Scattering data. The software enables data reduction from the 2D detector image, data manipulation and masking and provides analysis of 1D data by the Bayesian Indirect Fourier Transform.

yes yes yes

RCrane

- allows for semi-automated building of RNA structure within Coot.

yes yes yes

REDCAT

a residual dipolar coupling analysis tool. For-profit users interested in using this tool should contact Homayoun Valafar at hvalafar@gmail.com to inquire.

yes yes yes

Reduce

- 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.

yes yes yes

REFMAC

- 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. There are options to use different minimization methods. (At the moment only CGMAT is active.) REFMAC also produces an MTZ output file containing weighted coefficients for SigmaA weighted mFo-DFcalc and 2mFo-DFcalc maps, where missing data have been restored.

yes yes yes

relax

Molecular dynamics by NMR data analysis. relax is a program designed for the study of the dynamics of proteins or other macromolecules though the analysis of NMR relaxation experiments. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model and frame order dynamics theories using anisotropic NMR parameters such as RDCs and PCSs, and the investigation of stereochemistry.

yes yes yes

RELION

RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori (MAP) refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy. It is developed in the research group of Sjors Scheres at the MRC Laboratory of Molecular Biology. Briefly, the ill-posed problem of 3D-reconstruction is regularised by incorporating prior knowledge: the fact that macromolecular structures are smooth, i.e. they have limited power in the Fourier domain. Bayes' law uniquely determines how prior knowledge and experimental data are to be combined so that overfitting is reduced, and the optimal linear filter may be derived from the data without the need for arbitrary decisions or user expertise.

yes yes yes

Remediator

Remediator 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).

yes yes yes

REPLACE (GLRF and TF)

- 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.

yes yes yes

Ribbons

- a popular molecular graphics software display package.

yes yes yes

Ringer

- a program to detect molecular motions by automatic electron density sampling.

yes yes yes

rmeasure

rmeasure is a program for measuring the resolution of single-particle reconstructions.

yes yes yes

RMERGE

RMERGE can calculate 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.

yes yes yes

RnamlView

RnamlView is a visualization tool that displays/edits 2-dimensional diagrams of RNA/DNA secondary structures with tertiary interactions created by RNAView (above). The application generates standard molecular representations (e.g. tRNA cloverleaf structures) or any structural representation desired by the user 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.

yes yes yes

RNAView

- a program is developed to quickly display 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.

yes yes yes

Rosetta

- a software suite for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions. ROSETTA has been consistently successful in CASP and CAPRI competitions. Rosetta is also used for improving NMR and homology models before they are used in molecular replacement. Application developed and maintained by Baker Laboratory at the University of Washington.

yes yes yes

RSRef2000

- supports real-space simulated annealing refinement with X-ray data. RSRef uses 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. RSRef can be used to quickly pre-refine a protein structure during or after model building, or to completely refine structures with high non-crystallographic symmetry, that have good electron density. Application developed by Michael Chapman at Florida State University.

yes yes

Ruby

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.

yes yes yes

SAM

- a collection of tools for creating, refining, and using linear hidden Markov models for biological sequence analysis. The model states can be viewed as representing the sequence of columns in a multiple sequence alignment, with provisions for arbitrary position-dependent insertions and deletions in each sequence. The models are trained on a family of protein or nucleic acid sequences using an expectation-maximization algorithm and a variety of algorithmic heuristics. A trained model can then be used to both generate multiple alignments and search databases for new members of the family.

yes yes yes

saxsview

- 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.

yes yes yes

SCC

- a suite of programs for sequence alignment including: aln, swg, prrn, phyln and makmdm. aln: Pairwise alignment of biological sequences supporting spliced alignment procedures. swg: locally aligns a pair of DNA or protein sequences by Smith-Waterman-Gotoh algorithm. Currently spliced alignment is not supported. Profile version is very slow. prrn: global multiple alignment of a set of protein or DNA sequences by doubly nested iterative refinement method. phyln: UPGMA or NJ method to make a phylogenetic tree from a multiple alignment. makmdm: constructs binary PAM matrices. Must be run once before the first run of aln, swg or prrn.

yes yes yes

Schrodinger Suite

A suite of tools for small molecule drug discovery. The Schrodinger Suite runs on Linux and Mac workstations, but due to it’s size, it is not included in our default installation. To add Schrördinger to your installation, please email <bugs@sbgrid.org>.

yes yes yes

SCWRL3

- program for prediction of protein side-chain conformations.

yes yes

SCWRL4

- program for prediction of protein side-chain conformations.

yes yes yes

SHARP/autoSHARP

- an automated structure solution pipeline built around the heavy-atom refinement and phasing program SHARP, the density modification program SOLOMON, and the ARP/wARP package for automated model building and refinement (using REFMAC). It allows fully automated structure solution, from merged reflection data to an initial model, without any user intervention.

yes yes yes

SHELX-2013

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. SHELX was written and is actively maintained by George Sheldrick and his group at the University of Gottingen. SHELX-2013 is freely available to non-profit labs, but each lab must register with George Sheldrick before we can install the software. To include this software in your installation, please register [here][1] then send a copy of your registration confirmation to us at <licensing@sbgrid.org>. [1]: http://shelx.uni-ac.gwdg.de/SHELX/register.php

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SHELX-97

- 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. SHELX was written and is actively maintained by George Sheldrick and his group at the University of Gottingen. <br><br> This version of SHELX-97 is now obsolete and has been replaced by SHELX-2013. If you would like SHELX-2013 included in your installation, please see details on how to register <a href = "http://www.sbgrid.org/software/title/SHELX-2013">here</a>.

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SIGNATURE

- an automated particle selection system for electron microscopy. The application was written by James Chen in Niko Grigorieff laboratory at Brandeis.

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SIMPLE

Single-particle IMage Processing Linux Engine (SIMPLE) does ab initio 3D reconstruction (programs cluster & origami), heterogeneity analysis (programs cluster, origami & cycler), and high-resolution refinement (programs align, reconstruct, automask & cycler).The SIMPLE back-end consists of an object-oriented numerical library with a single external dependency - the Fastest Fourier Transform in the West (FFTW). The SIMPLE front-end consists of a few standalone, interoperable components developed according to the 'Unix toolkit philosophy'.

yes yes

Simulaid

A collection of utilities designed to help setting up and analyze molecular simulations.

yes yes

SITUS

- 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.

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SnB

- determination of the anomalously scattering substructures of selenomethionyl-substituted proteins containing as many as 160 Se sites. SnB is based on Shake-and-Bake, a dual-space direct-methods procedure.

yes yes yes

Solvate

- a program to construct an atomic solvent environment model for a given atomic macromolecule model (solute) for use in molecular dynamics simulations. Solvate generates irregularly-shaped solvent volumes, adapted to a given solute's structure; allows efficient computation of boundary forces as required in molecular dynamics simulations; guarantees a minimal solute-boundary-distance; allows to specify a minimum solvent surface curvature in order to avoid `flat' surface regions; generates `disordered' (= fluid) water, not a grid of water molecules (= ice); locally minimizes the positions of all water molecules; optionally places salt ions obeying a Debye-Hückel distribution; optionally places (and marks) buried water molecules; and is X-PLOR/CHARMm-compatible, i.e., input and output is in pdb-/psf-format.

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SOLVE/RESOLVE

- a program that can automatically search for heavy atom sites, calculate initial phases and perform density modification.

yes yes yes

SOMoRe

- 6D global search and multi-start optimization molecular replacement package.

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Sparky

- a graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers.

yes yes yes

SPARX

- (single particle analysis for resolution extension) is 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.

yes yes yes

SpecView

CcpNmr SpecView is designed to provide a fast way to visualise NMR spectrum and peak data. It supports 2D and 3D graphical display modes for multidimensional and simple 1D spectra. SpecView can automatically import spectra and peaks from many different file formats without user intervention. Spectra may be frequency referenced and superposed within the program.

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SPIDER

- (System for Processing Image Data from Electron microscopy and Related fields) is a large image processing suite for electron microscopy, developed over the last 23 years by Joachim Frank and his laboratory.

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Spire

- a graphical user interface for executing SPIDER batch files and other programs. It also offers a way to manage and organize the many output files created by SPIDER during reconstruction projects. Spire is designed to simplify running projects that consist of numerous SPIDER batch files. Users who are new to SPIDER can quickly start processing electron micrographs. Spire provides a convenient environment for testing and debugging batch files. However, Spire does not deal with program correctness per se; it simply runs your SPIDER procedure files, and saves a list of output files to a project file.

yes yes yes

SSAHA2

- (Sequence Search and Alignment by Hashing Algorithm) is 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.

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Staden

- a set of DNA sequence assembly, editing and analyzing tools. Developed at the Medical Research Council Laboratory of Molecular Biology, Cambridge, UK

yes yes yes

STAMP

- (STructural Alignment of Multiple Proteins) a suite of programs for the comparison and alignment of protein three dimensional structures. The suite will multiply align structures and produce a corresponding sequence alignment with confidence values associated with each aligned position. The software will also search a database of protein structures to identify structurally similar proteins. The suite includes a number of utility programs for the manipulation of protein structures.

yes yes yes

Suprim

- a 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.

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Surface Racer

- 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.

yes yes yes

SURFNET

- a program that generates surfaces, density contours and gap regions from coordinate data supplied in a PDB file.

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surfv

- 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.

yes yes yes

Swiss-PdbViewer

- an application that provides a user friendly interface allowing you to analyze several proteins at the same time.

yes yes yes

TALOS-N

TALOS-N: Prediction of Protein Backbone and Sidechain Torsion Angles from NMR Chemical Shifts

yes yes

T-Coffee

- a multiple sequence alignment package. You can use T-Coffee to align sequences or to combine the output of your favorite alignment methods (Clustal, Mafft, Probcons, Muscle...) into one unique alignment (M-Coffee).

yes yes yes

TENSOR

- allows the determination of rotational diffusion from three-dimensional structure coordinates and experimental 15N relaxation data, and nowallows 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 of anisotropic rotational diffusion tensor.

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The Image Processing Library & Toolbox (IPLT)

- a 2D Crystallography Suite developed by Andreas Schenk.

yes yes yes

Theseus

- a program that simultaneously superimposes multiple macromolecular structures. Instead of using the conventional least-squares criteria, Theseus finds the optimal solution to the superposition problem using the method of maximum likelihood. By downweighting variable regions of the superposition and by correcting for correlations among atoms, the ML superpositioning method produces much more accurate results.

yes yes yes

THREADER

- offers protein fold recognition by optimal protein sequence threading.

yes yes

Tiltpicker

- 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.

yes yes

TkDiff

tkdiff is 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.

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ULTRASCAN2

- a software package offering comprehensive analysis of hydrodynamic data from analytical ultracentrifugation experiments.

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ULTRASCAN3

- the latest multi-platform version of UltraScan, which is has now replaced the UltraScan II distribution. All users are encouraged to switch to UltraScan III for any new installations, since this software will be actively maintained, while UltraScan II development has stopped, although UltraScan II will continue to be available. Please note that if you want to view legacy data from UltraScan II, you will still need to install UltraScan II, since UltraScan III is not backward compatible with UltraScan II.

yes yes

UNIO

UNIO enables you to perform automated NMR data analysis for protein 3D structure determination. UNIO 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.

yes yes yes

Untangle

- 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.

yes yes

UROX

- designed for interactive fitting of high-resolution models (e.g, obtained by X-Ray crystallography) into Electron Microscopy reconstructions. It can also be used to fit two maps together (e.g., in tomography), or to perform Normal-modes calculations.

yes yes

USF Gerard Utilities

- the Swiss Army knife of crystallography tools. The installation includes the packages from RAVE, SBIN, X-UTIL, VOIDOO, DEJAVU and SPASM.

yes yes yes

VEDA

VEDA is 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.

yes yes

VMD

- a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

yes yes yes

vmd-xplor

The vmd-xplor package is 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. vmd-xplor is freely available to non-profit labs, but each lab must register with VMD before we can install the software. To include this software in your installation, please [register here][2], then send a copy of your registration confirmation to us at <licensing@sbgrid.org> [2]: http://vmd-xplor.cit.nih.gov/download/download.cgi

yes yes yes

WASP

- searches PDB files for misidentified water molecules that should be modeled as cations.

yes yes yes

Wattos

- 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.

yes yes

WHAT_CHECK

- the protein verification tool from the WHAT IF program available as a free stand-alone program, complete with all source code.

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WHATIF

- a general protein analysis program.

yes yes

X3D

X3D is a boxing program developed by James Conway. It contains a 'help'. If you are lazy, just do the following: Run X3D, and open a TIFF image file using the "File"->"Open Image" menu. Select a particle using the mouse. Then change the radius to a suitable value (the 'Pick radius' is just a visual help). When finished selecting particles, go to the "Preprocess"->"Parameters" menu and set all the parameters there. Important: Set "File Type" to EZD and use a reasonable box size. Go to the "Preprocess"->"Set Centering Parameters" menu and set the pixel size (in Angstroms); and set the remaining fields to 1 (we are not going to use them). Save the selected coordinates in a file .crd Select the Preprocess->Run menu item, this will extract, preprocess and save all the selected particles to image files.

yes yes yes

XDP

- used for processing Electron Diffraction data. Previously available only on DEC Alpha.

yes yes

XDrawChem

- 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.

yes yes

XDS

- X-ray Detector Software for processing single-crystal monochromatic diffraction data recorded by the rotation method. Written by Wolfgang Kabsch (see Tales about Developers section on SBGrid website).

yes yes yes

XDSAPP

- XDSAPP (Krug et al., 2012) is a graphical user interface for the easy and convenient processing of diffraction data sets using XDS. It is available for all our experimental end-stations. It automates the data processing and generates graphical plots of various data set statistics provided by XDS. By incorporating additional software, further information on certain features of the dataset, such as radiation decay or the presence of pseudo-translational symmetry and/or twinning is provided. Intensity files suitable for CCP4, SHELX and CNS are generated. <br><br> XDSAPP is freely available to non-profit labs, but each lab must register with Helmholtz-Zentrum Berlin before we can install the software. To include this software in your installation, please register here <a href = "http://www.helmholtz-berlin.de/forschung/oe/funkma/soft-matter/forschung/bessy-mx/xdsapp/download-registration_en.html">http://www.helmholtz-berlin.de/forschung/oe/funkma/soft-matter/forschung/bessy-mx/xdsapp/download-registration_en.html</a>, then send a copy of your registration confirmation to us at <a href = "mailto:licensing@sbgrid.org">licensing@sbgrid.org</a>. <br><br>

yes yes yes

XDSGUI

XDSGUI is a GUI (graphical user interface) for XDS that is supposed to help both novice and experienced users. It graphically displays the ASCII and cbf files that XDS writes, and can run useful shell commands with a simple mouse click. The design goal of the program is to enable XDS data processing without the command line, and to supply additional graphical information, in a simple, user-modifiable and user-extensible way.

yes yes yes

XDSi

- 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 package. Plots of the most informative statistics of INTEGRATE.LP, CORRECT.LP and XDSSTAT.LP are generated for each dataset. A plot comparing Rmeas, I/sig and Completeness of all the processed datasets is generated. You can also generate plots for datasets that have been processed using XDS without XDSi. Note that this software requires 'kpdf' to display its output.

yes yes yes

xdsme

xdsme is a collection of python scripts made to simplify the processing of crystal diffraction images with the XDS Program Package (X-ray Detector Software, http://xds.mpimf-heidelberg.mpg.de/). 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).

yes yes yes

XDSSTAT

- a home-brewn program that prints various statistics (that are not available from XDS itself) in the form of tables and images.

yes yes yes

XDS-Viewer

- an X-ray diffraction and control image viewing utility for data processed using the XDS program package.

yes yes yes

XEASY

- a program for interactive, computer-supported NMR spectrum analysis.

yes yes

XIA2

- an automated data reduction system designed to work from raw diffraction data and a little metadata, and produce usefully reduced data in a form suitable to immediately start phasing and structure solution, e.g. through Mr BUMP or your favorite experimental phasing suite.

yes yes yes

Xmipp

- (X-Window-based Microscopy Image Processing Package) a suite of image processing programs primarily aimed at single-particle 3D electron microscopy.

yes yes yes

Xplor-NIH

- a system for X-ray crystallography and NMR.

yes yes yes

XRayView

XRayView 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.

yes yes yes

xv

xv is an interactive image manipulation program for the X Window System. It can operate 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 if you have ghostscript (version 2.6 or above) installed on your machine, it can also display them.

yes yes yes

YUP

- (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.

yes yes yes

ZDOCK/RDOCK

- two protein docking algorithms designed to operate in succession. ZDOCK is a rigid-body docking program, and RDOCK is a refinement program. ZDOCK uses a fast Fourier transform to search all possible binding modes for proteins, evaluating based on shape complementarity, desolvation energy, and electrostatics. The top 2000 predictions from ZDOCK are then given to RDOCK where they are minimized by CHARMM to improve the energies and eliminate clashes, and then the electrostatic and desolvation energies are recomputed. From the Zhiping Lab at Boston University. by RDOCK.

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Zephyr

- 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. Zephyr was written (is being written) by Alex Stewart and Donald J. Olbris in the laboratories of Prof. David J. DeRosier and Prof. Niko Grigorieff at the Rosenstiel Basic Medical Sciences Research Center at Brandeis University in Waltham, Massachusetts, USA.

yes yes

ZINC

a free database of commercially-available compounds for virtual screening. ZINC contains over 21 million purchasable compounds in ready-to-dock, 3D formats. ZINC is provided by the Shoichet Laboratory in the Department of Pharmaceutical Chemistry at the University of California, San Francisco (UCSF). To cite ZINC, please reference: Irwin, Sterling, Mysinger, Bolstad and Coleman, J. Chem. Inf. Model. 2012 DOI: 10.1021/ci3001277. The original publication is Irwin and Shoichet, J. Chem. Inf. Model. 2005;45(1):177-82 PDF, DOI. We thank NIGMS for financial support (GM71896).