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

Developers

Henning Stahlberg

Categories

Electron Microscopy

Versions

• Linux 32: 3.4.1
• Linux 64: 3.4.1
• OSX Intel: 3.4.1
• OSX PPC: 3.0.6

Citations

Gipson et al. 2dx--user-friendly image processing for 2D crystals. J Struct Biol (2007) vol. 157 (1) pp. 64-72

• 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.

Developers

Wilma Olson

Xiang-Jun Lu

Categories

X-ray Crystallography

Structure Analysis

Structure Visualization

Nucleic Acids

Versions

• Linux 32: 2.1b-20130222
• Linux 64: 2.1b-20130222
• OSX Intel: 2.1b-20130222
• OSX PPC: 2.0
• SGI Irix: 1.5

Citations

Xiang-Jun Lu and Wilma K Olson (2008) "3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures." Nature Protocols, 3, 1213-1227.

• 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.

Developers

Andy Arvai

Categories

X-ray Crystallography

Versions

• Linux 32: 1.9.8
• Linux 64: 1.9.8
• OSX Intel: 1.9.8
• OSX PPC: 1.9.8

Technical Notes

Adxv will display data from most current detectors:

• ADSC ccd
• Mar ccd
• APS 3x3 ccd
• Mar image plate (old and new format)
• Raxis II & IV
• Fuji image plate
• Crystallographic Binary Format (CBF)
• XDS .pck files
• Raw binary 8, 16 & 32 bit integer data

• 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.

Developers

Charlie Bond

Categories

Bioinformatics

Versions

• Linux 32: 1.0.025
• Linux 64: 1.0.025
• OSX Intel: 1.0.025
• OSX PPC: 1.0.025

Citations

Bond, C.S. and Schüttelkopff, A.W. (2009), Acta cryst. D65, 510-512

• 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.

Developers

Levan Wadley

Amelia Johnson

Anna Pyle

Kevin Keating

Categories

Nucleic Acids

Versions

• Linux 32: 1.0.1
• Linux 64: 1.0.1
• OSX Intel: 1.0.1
• OSX PPC: 1.0.1

Citations

Duarte and Pyle. Stepping through an RNA structure: A novel approach to conformational analysis. J Mol Biol. 1998. 284(5):1465-78.

• 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.

Developers

Michael Holst

Nathan Baker

Categories

Structure Analysis

Versions

• Linux 32: 1.4.0
• Linux 64: 1.4.0
• OSX Intel: 1.4.0
• OSX PPC: 1.2.1

Citations

Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001.

an interpretation of crystallographic electron density maps and automatic construction and refinement of macromolecular models.

This software is licensed on a per-lab basis. Please visit the ARP/wARP website to request a license, and then email help@sbgrid.org to have it added to your installation.

The following authors developed this software: Victor Lamzin, Gerrit Langer, Ciaran Carolan, Saul Hazledine, Philipp Heuser, Tim Wiegels, Anastassis Perrakis, Krista Joosten.

Developers

Martin Raditsch

Anastassis Perrakis

Victor Lamzin

Categories

X-ray Crystallography

Versions

• Linux 32: 7.3
• Linux 64: 7.3
• OSX Intel: 7.3
• OSX PPC: 7.1.1
• SGI Irix: 6.1.1

Citations

Langer et al. Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nat Protoc (2008) vol. 3 (7) pp. 1171-9

• a program suite for small-angle scattering (SAXS) data analysis from biological macromolecules.

This software is licensed on a per-lab basis. Please visit the BEST website to request a license, and then email help@sbgrid.org to have it added to your installation.

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

Developers

Dmitri Svergun

Maxim Petoukhov

Martin Raditsch

Categories

SAXS

Versions

• Linux 32: 2.5.1
• Linux 64: 2.5.1
• OSX Intel: 2.5.1
• OSX PPC: 2.2

Citations

PRIMUS, MIXTURE: Konarev. PRIMUS - a Windows-PC based system for small-angle scattering data analysis. J Appl Cryst. 2003. 36:1277-1282.

GNOM: Svergun. Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J. Appl. Crystallogr. 1992. 25:495-503.

DAMMIN, MONSA: Svergun. Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys J. 1999. 2879-2886.

DAMMIF: Franke and Svergun.DAMMIF, a program for rapid ab-initio shape determination in small-angle scattering. J. Appl. Cryst. 2009. 42:342-346.

SASREF, BUNCH, CORAL, GLOBSYMM: Petoukhov and Svergun. Global rigid body modelling of macromolecular complexes against small-angle scattering data. Biophys. J. 2005. 89:1237-1250.

MASSHA: Konarev et al. MASSHA - a graphic system for rigid body modelling of macromolecular complexes against solution scattering data. J Appl Cryst. 2001. 34:527-532.

EOM: Bernado et al. Structural Characterization of Flexible Proteins Using Small-Angle X-ray Scattering. J. Am. Chem. Soc. 2007. 129(17):5656-5664.

CRYSOL, CRYSON, : Svergun et al. CRYSOL - a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates J. Appl. Cryst. 1995. 28:768-773.

SUPCOMB: Kozin & Svergun. Automated matching of high- and low-resolution structural models J Appl Cryst. 2000. 34:33-41.

DAMAVER: Volkov and Svergun. Uniqueness of ab-initio shape determination in small-angle scattering. J. Appl. Cryst. 2003. 36:860-864.

DARA: Sokolova et al. Prototype of a database for rapid protein classification based on solution scattering data. J. Appl. Cryst. 2003. 36:865-868.

• 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).

Developers

Giovanni Cardone

Timothy Baker

Categories

Electron Microscopy

Versions

• Linux 32: 4.02
• Linux 64: 4.02
• OSX Intel: 4.02
• OSX PPC: 3.08

Citations

Yan X., R.S. Sinkovits, and T.S. Baker (2007) AUTO3DEM - an automated and high throughput program for image reconstruction of icosahedral particles. J. Struct. Bio. 157:73-82.

• 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.

Developers

Art Olson

Richard Belew

William Hart

Scott Kurowski

David Goodsell

Garrett Morris

Categories

Computational Chemistry

Versions

• Linux 32: 4.2.3
• Linux 64: 4.2.3
• OSX Intel: 4.2.3
• OSX PPC: 4.2.3

Citations

Cosconati et al. Virtual Screening with AutoDock: Theory and Practice. Expert opinion on drug discovery (2010) vol. 5 (6) pp. 597-607

• 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.

Developers

Oleg Trott

Categories

Computational Chemistry

Versions

• Linux 32: 1.1.2
• Linux 64: 1.1.2
• OSX Intel: 1.1.2
• OSX PPC: 1.1.1

Citations

Trott and Olson. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem (2010) vol. 31 (2) pp. 455-61

• 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.

Developers

Fei Long

Garib Murshudov

Categories

X-ray Crystallography

Versions

• Linux 32: 1.0.0
• Linux 64: 1.0.0
• OSX Intel: 1.0.0
• OSX PPC: 1.0.0

Citations

Long et al. BALBES: a molecular-replacement pipeline. Acta Crystallogr D Biol Crystallogr (2008) vol. 64 (Pt 1) pp. 125-32

• a program for optimal planning of X-ray data collection from protein crystals.

This software is licensed on a per-lab basis. Please visit the BEST website to request a license, and then email help@sbgrid.org to have it added to your installation.

Developers

Gleb Bourenkov

Alexander Popov

Martin Raditsch

Categories

X-ray Crystallography

Versions

• Linux 32: 3.4.4
• Linux 64: 3.4.4
• OSX Intel: 3.2.0
• OSX PPC: 3.2.0

Citations

Bourenkov and Popov. Optimization of data collection taking radiation damage into account. Acta Crystallogr D Biol Crystallogr (2010) vol. 66 (Pt 4) pp. 409-19

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

Categories

Utilities

Versions

• Linux 32: 1.6.0
• Linux 64: 1.6.0
• OSX Intel: 1.6.0
• OSX PPC: 1.6.0

Citations

Stajich et al. The Bioperl Toolkit: Perl modules for the life sciences. Genome Research. 2002. 12(10):1611-8.

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

Categories

Utilities

Versions

• Linux 32: 1.54
• Linux 64: 1.54
• OSX Intel: 1.54
• OSX PPC: 1.54

Citations

Cock et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics. 2009. 25(11):1422-3.

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

Categories

Bioinformatics

Versions

• Linux 32: 2.2.26
• Linux 64: 2.2.26
• OSX Intel: 2.2.26
• OSX PPC: 2.2.22

Citations

Altschul et al. Basic local alignment search tool. J Mol Biol (1990) vol. 215 (3) pp. 403-10

Technical Notes

Full Blast database documentation is here: ftp://ftp.ncbi.nlm.nih.gov/blast/db/blastdb.html

Pre-formatted databases must be downloaded using the update_blastdb.pl script or via FTP in binary mode. Documentation for the update_blastdb.pl script can be obtained by running the script without any arguments (perl is required).

The compressed files downloaded must be inflated with gzip or other decompress tools. The BLAST database files can then be extracted out of the resulting tar file using tar program on Unix/Linux or WinZip and StuffIt Expander on Windows and Macintosh platforms, respectively.

Large databases are formatted in multiple 1 Gigabytes volumes, which are named using the database.##.tar.gz convention. All relevant volumes are required. An alias file is provided so that the database can be called using the alias name without the extension (.nal or .pal). For example, to call est database, simply use "-d est" option in the commandline (without the quotes).

Certain databases are subsets of a larger parental database. For those databases, alias and mask files, rather than actual databases, are provided. The mask file needs the parent database to function properly. The parent databases should be generated on the same day as the mask file. For example, to use swissprot pre-formatted database, swissprot.tar.gz, one will need to get the nr.tar.gz with the same date stamp.

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

Developers

William Furey

Charles Weeks

Categories

X-ray Crystallography

Versions

• Linux 32: 1.02
• Linux 64: 1.02
• OSX PPC: 1.02

Technical Notes

Test the package with BnP test data (can be downloaded from BnP web page)

• an extension to Molscript

Developers

Robert Esnouf

Categories

Structure Visualization

Versions

• Linux 32: 2.6b
• Linux 64: 2.6b
• OSX Intel: 2.6b
• OSX PPC: 2.6b
• SGI Irix: 2.6b

Citations

Esnouf, R. M. (1999) Acta Crystallographica, D55, 938-940.
Esnouf, R. M. (1997) Journal of Molecular Graphics, 15, 132-134.
Kraulis, P. J. (1991) Journal of Applied Crystallography, 24, 946-950.

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

Developers

Bernard Heymann

Categories

Electron Microscopy

Versions

• Linux 32: 1.8.6
• Linux 64: 1.8.6
• OSX Intel: 1.8.6
• OSX PPC: 1.7.0
• SGI Irix: 0.8

Citations

Heymann and Belnap. Bsoft: image processing and molecular modeling for electron microscopy. J Struct Biol (2007) vol. 157 (1) pp. 3-18

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

Developers

Pascal Bettendorff

Rochus Keller

Fred Damberger

Categories

NMR Methods

Versions

• Linux 32: 1.8.4
• Linux 64: 1.8.4
• OSX Intel: 1.8.4
• OSX PPC: 1.8.4

Citations

Please reference the book The Computer Aided Resonance Assignment Tutorial by Rochus Keller. Alternatively you can cite Rochus' PhD thesis, Diss. ETH Nr. 15947. It would also be helpful if you could mention in your publication that CARA can be downloaded from cara.nmr.ch

• (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.

All SBGrid members must complete the CCP4 license and return the executed document directly to The Science and Technology Facilities Council as specified on the CCP4 licensing page located here: http://www.ccp4.ac.uk/ccp4license.php.

Developers

Ronan Keegan

Charles Ballard

Categories

X-ray Crystallography

Versions

• Linux 32: 6.3.0
• Linux 64: 6.3.0
• OSX Intel: 6.3.0
• OSX PPC: 6.1.13
• SGI Irix: 5.0.2

Citations

CCP4: COLLABORATIVE COMPUTATIONAL PROJECT, NUMBER 4. 1994. The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst. D50, 760-763.

Winn et al. Overview of the CCP4 suite and current developments. Acta Crystallogr D Biol Crystallogr (2011) vol. 67 (Pt 4) pp. 235-42

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

Developers

Liz Potterton

Stuart McNicholas

Categories

Structure Visualization

Versions

• Linux 32: 2.7.3
• Linux 64: 2.7.3
• OSX Intel: 2.7.3
• OSX PPC: 2.1.0

Citations

Potterton et al. Developments in the CCP4 molecular-graphics project. Acta Crystallogr D Biol Crystallogr (2004) vol. 60 (Pt 12 Pt 1) pp. 2288-94

• 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).

Developers

Wayne Boucher

Rasmus Fogh

Categories

NMR Methods

Versions

• Linux 32: 2.2.1
• Linux 64: 2.2.1
• OSX Intel: 2.2.1
• OSX PPC: 2.1.5

Citations

Vranken et al. The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins (2005) vol. 59 (4) pp. 687-96

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

Developers

Thomas Goddard

Greg Couch

Tom Ferrin

Categories

Structure Visualization

Versions

• Linux 32: 1.6.2
• Linux 64: 1.6.2
• OSX Intel: 1.6.2
• OSX PPC: 1.4.1
• SGI Irix: 1.170

Citations

Pettersen et al. UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem (2004) vol. 25 (13) pp. 1605-12

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

Developers

Clustal Developer Group

Categories

Bioinformatics

Versions

• Linux 32: 2.1
• Linux 64: 2.1
• OSX Intel: 2.1
• OSX PPC: 2.1

Citations

Chenna et al. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res (2003) vol. 31 (13) pp. 3497-500

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

Developers

Axel Brunger

Categories

X-ray Crystallography

Versions

• Linux 32: 1.3r8
• Linux 64: 1.3r8
• OSX Intel: 1.3r8
• OSX PPC: 1.3
• SGI Irix: 1.1

Citations

Brunger. Version 1.2 of the Crystallography and NMR system. Nat Protoc (2007) vol. 2 (11) pp. 2728-33

Brünger et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr (1998) vol. 54 (Pt 5) pp. 905-21

• (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.

Developers

Paul Emsley

Categories

X-ray Crystallography

Versions

• Linux 32: 0.7
• Linux 64: 0.7
• OSX Intel: 0.7.0-1
• OSX PPC: 0.6.2-pre-1-65
• SGI Irix: 0.0.33

Citations

Emsley et al. Features and development of Coot. Acta Crystallogr D Biol Crystallogr (2010) vol. 66 (Pt 4) pp. 486-501

Emsley and Cowtan. Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr (2004) vol. 60 (Pt 12 Pt 1) pp. 2126-32

Technical Notes

Versions later than 0.3.3 will not work on Fedora Core 3 or older machines due to a change in the GLIBC ABI.

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

Developers

Richard Lavery

Categories

Structure Analysis

Nucleic Acids

Versions

• Linux 32: 5.3
• Linux 64: 5.3
• OSX Intel: 5.3
• OSX PPC: 5.3

Citations

Lavery and Sklenar. Defining the structure of irregular nucleic acids: conventions and principles. J Biomol Struct Dyn (1989) vol. 6 (4) pp. 655-67

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

Developers

Richard Lavery

Categories

Structure Analysis

Nucleic Acids

Versions

• Linux 32: 1.0
• Linux 64: 1.0
• OSX Intel: 1.0
• OSX PPC: 1.0

Citations

Lavery et al. Conformational analysis of nucleic acids revisited: Curves+. Nucleic Acids Res (2009) vol. 37 (17) pp. 5917-29

A program for calculating protein electrostatics.

This software requires a separate license. Please request a license on the DelPhi website: http://bhapp.c2b2.columbia.edu/software/cgi-bin/software.pl?input=DelPhi and then send the license email to help@sbgrid.org to request installation for your site.

Developers

Barry Honig

Categories

Structure Analysis

Versions

• Linux 32: 1.1
• Linux 64: 1.1
• OSX Intel: 1.1
• OSX PPC: 1.1

Citations

Rocchia et al. Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: applications to the molecular systems and geometric objects. J Comput Chem (2002) vol. 23 (1) pp. 128-37

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

Developers

Dino Support

Ansgar Philippsen

Categories

Structure Visualization

Versions

• Linux 32: 0.9.4
• Linux 64: 0.9.4a
• OSX Intel: 0.9.4
• OSX PPC: 0.9.0
• SGI Irix: 0.9.0

Citations

How to reference DINO:
If a figure is produced with DINO, please cite either underneath the figure itself, as a standalone reference, or in Materials and Methods (usually items i and iii are the best choice):

(i) underneath Figure Figure created with DINO (http://www.dino3.org)

(ii) as reference Figure created with DINO#

Ansgar Philippsen, http://www.dino3d.org

(iii) in Material and Methods [...] Figures #, # and # were created using DINO (http://www.dino3d.org).

• 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.

Developers

Scott Brozell

Dock licensor

Categories

Computational Chemistry

Versions

• Linux 32: 6.5
• Linux 64: 6.5
• OSX Intel: 6.5
• OSX PPC: 5.4.0
• SGI Irix: 4.0.1

Citations

Lang et al. DOCK 6: combining techniques to model RNA-small molecule complexes. RNA (2009) vol. 15 (6) pp. 1219-30

Moustakas et al. Development and validation of a modular, extensible docking program: DOCK 5. J Comput Aided Mol Des (2006) vol. 20 (10-11) pp. 601-19

• 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

Developers

Gert Vriend

Categories

Structure Analysis

Versions

• Linux 32: 2.1.0
• Linux 64: 2.1.0
• OSX Intel: 2.1.0
• OSX PPC: 20060404
• SGI Irix: april2000

Citations

Kabsch and Sander. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers (1983) vol. 22 (12) pp. 2577-637

• 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.

Developers

Steven Hayward

Versions

• Linux 32: 1.01
• Linux 64: 1.01
• OSX Intel: 1.01
• OSX PPC: 1.01

Citations

Poornam et al. A method for the analysis of domain movements in large biomolecular complexes. Proteins (2009) vol. 76 (1) pp. 201-12

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

Developers

Giovanni Cardone

Categories

Tomography

Versions

• Linux 32: 0.5.2
• Linux 64: 0.5.2
• OSX Intel: 0.5.2
• OSX PPC: 0.5.2

Citations

Cardone et al. A resolution criterion for electron tomography based on cross-validation. Journal of structural biology (2005) vol. 151 (2) pp. 117-29

Technical Notes

The website for this application is no longer available.

• 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.

Developers

Tom Alber

Categories

X-ray Crystallography

Versions

• Linux 32: 1.3.6.1.2
• Linux 64: 1.3.6.1.2
• OSX Intel: 1.3.6.1.2
• OSX PPC: 1.3.6.1.1

Citations

Holton and Alber. Automated protein crystal structure determination using ELVES. Proceedings of the National Academy of Sciences of the United States of America (2004) vol. 101 (6) pp. 1537-42

• 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.

Developers

Steven Ludtke

Categories

Electron Microscopy

Versions

• Linux 32: 1.9
• Linux 64: 1.9
• OSX Intel: 1.9
• OSX PPC: 1.9

Citations

Ludtke. 3-D structures of macromolecules using single-particle analysis in EMAN. Methods in molecular biology (Clifton, NJ) (2010) vol. 673 pp. 157-73

Technical Notes

there still seem to be some problems running under RH9 with Gnome. KDE has no problems Note: Under OS X, the main windows will get locked behind other "Aqua" windows. This is a bug in the way they programmed the forms with Qt.

• 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.

Developers

Steven Ludtke

Categories

Electron Microscopy

Tomography

Versions

• Linux 32: 2.06
• Linux 64: 2.06
• OSX Intel: 2.06
• OSX PPC: 20090618

Citations

Tang et al. EMAN2: an extensible image processing suite for electron microscopy. Journal of structural biology (2007) vol. 157 (1) pp. 38-46

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

Developers

Alan Bleasby

Peter Rice

Categories

Bioinformatics

Utilities

Versions

• Linux 32: 6.4.0
• Linux 64: 6.4.0
• OSX Intel: 6.4.0
• OSX PPC: 6.3.1

Citations

Olson. EMBOSS opens up sequence analysis. European Molecular Biology Open Software Suite. Briefings in bioinformatics (2002) vol. 3 (1) pp. 87-91

• 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.

Developers

Yousif Shamoo

Categories

Structure Analysis

Nucleic Acids

Versions

• Linux 32: 1.0
• Linux 64: 1.0
• OSX Intel: 1.0
• OSX PPC: 1.0

Citations

Allers and Shamoo. Structure-based analysis of protein-RNA interactions using the program ENTANGLE. Journal of molecular biology (2001) vol. 311 (1) pp. 75-86

Technical Notes

Not all PDBs work with this program.

Some example PDBs that work:
1URW
1CVJ

• 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.

Developers

William Pearson

Categories

Bioinformatics

Versions

• Linux 32: 35.4.3
• Linux 64: 35.4.3
• OSX Intel: 35.4.3
• OSX PPC: 35.4.3

Citations

Mount. Using a FASTA Sequence Database Similarity Search. CSH protocols (2007) vol. 2007 pp. pdb.top16

Pearson. Rapid and sensitive sequence comparison with FASTP and FASTA. Methods in enzymology (1990) vol. 183 pp. 63-98

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.

Developers

Geospiza support

Versions

• Linux 32: 1.3.1
• Linux 64: 1.3.1
• OSX Intel: 1.5.0
• OSX PPC: 1.4.0

• (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.

Developers

Nikolaus Grigorieff

Categories

Electron Microscopy

Versions

• Linux 32: 8.11
• Linux 64: 8.11
• OSX Intel: 8.11
• OSX PPC: 8.09

Citations

Grigorieff. FREALIGN: high-resolution refinement of single particle structures. Journal of structural biology (2007) vol. 157 (1) pp. 117-25

Li et al. GPU-enabled FREALIGN: accelerating single particle 3D reconstruction and refinement in Fourier space on graphics processors. Journal of structural biology (2010) vol. 172 (3) pp. 407-12

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

Categories

Utilities

Versions

• Linux 32: 9.04
• Linux 64: 9.04
• OSX Intel: 9.04
• OSX PPC: 8.61

• 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.

Categories

Utilities

Versions

• Linux 32: 4.6.0
• Linux 64: 4.6.0
• OSX Intel: 4.6.0
• OSX PPC: 4.2.6

Citations

Williams and Kelley. Gnuplot 4.5: an interactive plotting program. 2011. URL http://gnuplot.info. (Last accessed: YEAR MONTH DAY)

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

Categories

Utilities

Versions

• Linux 32: 5.1.22
• Linux 64: 5.1.22
• OSX Intel: 5.1.22
• OSX PPC: 5.1

Citations

No reference, please just refer website when citing: http://plasma-gate.weizmann.ac.il/Grace/

Technical Notes

Requires X11 on Mac OS X.

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

Developers

Yifan Hu

Stephen North

John Ellson

Arif Bilgin

Emden Gansner

Graphviz

Categories

Utilities

Versions

• Linux 32: 2.28.0
• Linux 64: 2.28.0
• OSX Intel: 2.28.0
• OSX PPC: 2.14

Citations

Ellson et al. Graphviz and Dynagraph -- Static and Dynamic Graph Drawing Tools. in: Graph Drawing Software. 2004. eds:M. Junger and P. Mutzel. Springer-Verlag. 127-148.

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

Developers

Nikolaus Grigorieff

Categories

Electron Microscopy

Versions

• Linux 32: 20110914
• Linux 64: 20110914
• OSX Intel: 20110914
• OSX PPC: 20100726

Citations

ctffind and ctftilt: Mindell and Grigorieff. Accurate determination of local defocus and specimen tilt in electron microscopy. J Struct Biol. 2003. 142:334-47.

rmeasure: Sousa and Grigorieff. Ab initio resolution measurement for single particle structures. J Struct Biol. 2007. 157:201-10.

• 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.

Developers

Matteo Frigo

Steven Johnson

Categories

Computational Chemistry

Versions

• Linux 32: 4.6
• Linux 64: 4.6
• OSX Intel: 4.6
• OSX PPC: 4.0.5

Citations

Van Der Spoel et al. GROMACS: fast, flexible, and free. Journal of computational chemistry (2005) vol. 26 (16) pp. 1701-18

• (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.

Developers

Alexandre Bonvin

Categories

NMR Methods

Computational Chemistry

Versions

• Linux 32: 2.1
• Linux 64: 2.1
• OSX Intel: 2.1
• OSX PPC: 2.1

Citations

de Vries et al. HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets. Proteins (2007) vol. 69 (4) pp. 726-33

Dominguez et al. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. Journal of the American Chemical Society (2003) vol. 125 (7) pp. 1731-7

• 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. The newest version, HKL3000, supports all steps of the structure determination process. HKL was developed and is maintained by Wladek Minor (University of Virginia).

Categories

X-ray Crystallography

Versions

• Linux 32: 2000.0.98.704k
• Linux 64: 2000.0.98.704k
• OSX Intel: 2000.0.98.704k
• OSX PPC: HKL2000_mac_0.692i

Citations

Minor et al. HKL-3000: the integration of data reduction and structure solution--from diffraction images to an initial model in minutes. Acta crystallographica Section D, Biological crystallography (2006) vol. 62 (Pt 8) pp. 859-66

Technical Notes

Once you have received your license file from HKL Software, copy the file to /usr/local/lib/cr_info and the HKL2000 package will start working.

The default directory for detector profiles is $HOME/hklint. To override this default and use your own detector profiles, set the HKLPATH variable to the directory containing your detector profiles after sourcing an SBGrid shell initialization file.

The HKLPATH line will override the defaults for your site.

• a graphical user-interface for macromolecular phasing.

Developers

Thomas Schneider

Categories

X-ray Crystallography

Versions

• Linux 32: 0.2
• Linux 64: 0.2
• OSX Intel: 0.2
• OSX PPC: 0.2

Citations

Thomas Pape & Thomas R. Schneider HKL2MAP: a graphical user interface for phasing with SHELX programs. J. Appl. Cryst. 2004. 37:843-844.

Technical Notes

To use HKL2MAP, you need to have licenced versions of SHELXC/D/E and Xfit in the executable path of your computer.

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

Categories

Utilities

Versions

• Linux 32: 6.7.1-6
• Linux 64: 6.7.1-6
• OSX Intel: 6.7.1-6
• OSX PPC: 6.3.3

• 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.

Developers

David Mastronarde

Categories

Electron Microscopy

Tomography

Versions

• Linux 32: 4.5.2
• Linux 64: 4.5.2
• OSX Intel: 4.5.2
• OSX PPC: 4.1.9

Citations

Kremer et al. Computer visualization of three-dimensional image data using IMOD. J Struct Biol (1996) vol. 116 (1) pp. 71-6

Mastronarde. Dual-axis tomography: an approach with alignment methods that preserve resolution. J Struct Biol (1997) vol. 120 (3) pp. 343-52

• 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.

Developers

Harry Powell

Categories

X-ray Crystallography

Versions

• Linux 32: 1.0.7
• Linux 64: 1.0.7
• OSX Intel: 1.0.7
• OSX PPC: 1.0.5

Citations

Battye et al. iMOSFLM: a new graphical interface for diffraction-image processing with MOSFLM. Acta Crystallogr D Biol Crystallogr (2011) vol. 67 (Pt 4) pp. 271-81

• 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.

Developers

Geoff Barton

Categories

Bioinformatics

Versions

• Linux 32: 2.8
• Linux 64: 2.8
• OSX Intel: 2.8
• OSX PPC: 2.6.1

Citations

Clamp et al. The Jalview Java alignment editor. Bioinformatics (2004) vol. 20 (3) pp. 426-7

Waterhouse et al. Jalview Version 2--a multiple sequence alignment editor and analysis workbench. Bioinformatics (2009) vol. 25 (9) pp. 1189-91

• a program for automatically plotting protein-ligand interactions.

Developers

Marina Santilli

Roman Laskowski

Categories

Structure Analysis

Versions

• Linux 32: 4.5.3
• Linux 64: 4.5.3
• OSX Intel: 4.5.3
• OSX PPC: 4.5.3

Citations

Wallace et al. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng (1995) vol. 8 (2) pp. 127-34

• 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.

Developers

Dan Strahs

Tamar Schlick

Categories

Structure Analysis

Nucleic Acids

Versions

• Linux 32: 1.0
• Linux 64: 1.0
• OSX PPC: 1.0

Citations

Barbic and Crothers. Comparison of analyses of DNA curvature. J Biomol Struct Dyn (2003) vol. 21 (1) pp. 89-97

• 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.

Developers

Katoh Kazutaka

Categories

Bioinformatics

Versions

• Linux 32: 7.032
• Linux 64: 7.032
• OSX Intel: 7.032
• OSX PPC: 6.846

Citations

Katoh et al. Multiple alignment of DNA sequences with MAFFT. Methods Mol Biol (2009) vol. 537 pp. 39-64

Katoh and Toh. Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinformatics (2008) vol. 9 (4) pp. 286-98

• 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.

Developers

Ugo Bastolla Bufalini

Categories

Structure Analysis

Versions

• Linux 32: 1.0
• Linux 64: 1.0
• OSX Intel: 1.0
• OSX PPC: 1.0

Citations

Lupyan et al. A new progressive-iterative algorithm for multiple structure alignment. Bioinformatics. 2005. 21(15):3255-63.

• 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.

Developers

Cowen

Matthew Menke

Categories

Bioinformatics

Versions

• Linux 32: 1.00
• Linux 64: 1.00
• OSX Intel: 1.00
• OSX PPC: 1.00

Citations

Menke et al. Matt: local flexibility aids protein multiple structure alignment. PLoS Comput Biol (2008) vol. 4 (1) pp. e10

• 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.

Developers

RCSB Developer Group

Categories

Structure Analysis

Versions

• Linux 32: 8.120
• Linux 64: 8.120
• OSX Intel: 8.120
• OSX PPC: 8.061

• 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.

Developers

MCCE Developer Group

Marilyn Gunner

Categories

Structure Analysis

Versions

• Linux 32: 2.2
• Linux 64: 2.2
• OSX Intel: 2.2
• OSX PPC: 2.2

Citations

Song et al. MCCE2: improving protein pKa calculations with extensive side chain rotamer sampling. Journal of computational chemistry (2009) vol. 30 (14) pp. 2231-47

• (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.

Developers

Michal Hammel

Categories

SAXS

Versions

• Linux 32: 20101116
• Linux 64: 20101116
• OSX Intel: 20101116
• OSX PPC: 20101116

Citations

Bernadó et al. Structural characterization of flexible proteins using small-angle X-ray scattering. Journal of the American Chemical Society (2007) vol. 129 (17) pp. 5656-64

Pelikan et al. Structure and flexibility within proteins as identified through small angle X-ray scattering. General physiology and biophysics (2009) vol. 28 (2) pp. 174-89

• 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.

  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.

  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.

  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.

Developers

Michael Sanner

Arthur Olson

Categories

Structure Visualization

Utilities

Versions

• Linux 32: 1.5.6rc3
• Linux 64: 1.5.6rc3
• OSX Intel: 1.5.6rc3
• OSX PPC: 1.5.4

Citations

ADT: Sanner. Python: A Programming Language for Software Integration and Development. J. Mol. Graphics Mod. 1999. 17:57-61.

isocontour: Bajaj et al. Fast IsoContouring for Improved Interactivity, Proceedings of ACM Siggraph/IEEE Symposium on Volume Visualization, ACM Press, 1996, pages 39 - 46, San Francisco, CA

msms: Sanner et al. Reduced surface: an efficient way to compute molecular surfaces. Biopolymers. 1996. 38(3):305-320.

PCVolRen: Bajaj et al. A Parallel Multi-PC Volume Rendering System, ICES and CS Technical Report, University of Texas, 2002.

Pmv: Sanner. Python: A Programming Language for Software Integration and Development. J. Mol. Graphics Mod. 1999. 17:57-61.

vision: Sanner et al. ViPEr a Visual Programming Environment for Python. 10th International Python Conference, February 2002.

• 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.

Developers

Ben Webb

Categories

Computational Chemistry

Versions

• Linux 32: 9.11
• Linux 64: 9.11
• OSX Intel: 9.11
• OSX PPC: 9v9

Citations

Eswar et al. Protein structure modeling with MODELLER. Methods in molecular biology (Clifton, NJ) (2008) vol. 426 pp. 145-59

Eswar et al. Comparative protein structure modeling using MODELLER. Current protocols in protein science / editorial board, John E Coligan [et al] (2007) vol. Chapter 2 pp. Unit 2.9

Technical Notes

No graphical interface. To start the program type 'modeller'. There are some tutorials to get you started available at http://salilab.org/modeller/tutorial/ .

• 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.

Developers

Martin Blackledge

Categories

NMR Methods

Versions

• Linux 32: 2.0
• Linux 64: 2.0
• OSX Intel: 1.0
• OSX PPC: 1.0

Citations

1.0: Dosset et al. Novel Interactive Tool for Rigid-Body Modeling of Multi-Domain Macromolecules using Residual Dipolar Couplings. J.Biomol. NMR. 2001. 20:223-231.

2.0: Dosset et al. Efficient analysis of macromolecular rotational diffusion from heteronuclear relaxation data. Biomol.NMR. 2000. 16: 23-28.

• 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.

Developers

Michal Otyepka

Martin Petrek

Categories

Structure Analysis

Versions

• Linux 32: 1.2
• Linux 64: 1.2
• OSX Intel: 1.2
• OSX PPC: 1.2

Citations

Petrek et al. MOLE: a Voronoi diagram-based explorer of molecular channels, pores, and tunnels. Structure (London, England : 1993) (2007) vol. 15 (11) pp. 1357-63

Petrek et al. CAVER: a new tool to explore routes from protein clefts, pockets and cavities. BMC bioinformatics (2006) vol. 7 pp. 316

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

Developers

Sharron Thomas

Kurt Wuthrich

Categories

Structure Visualization

Versions

• Linux 32: 2k.2.0
• Linux 64: 2k.2.0
• OSX Intel: 2k.2.0
• OSX PPC: 2k.2.0
• SGI Irix: 2k.1.0

Citations

Koradi et al. MOLMOL: a program for display and analysis of macromolecular structures. Journal of molecular graphics (1996) vol. 14 (1) pp. 51-5, 29-32

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

Developers

Masami Hasegawa

Institute for Statistical Mathematics software & Data Library

Jun Adachi

Categories

Bioinformatics

Versions

• Linux 32: 2.3b3
• Linux 64: 2.3b3
• OSX Intel: 2.3b3
• OSX PPC: 2.3b3
• SGI Irix: 2.3b3

Citations

ADACHI, J., & HASEGAWA, M. MOLPHY, programs for molecular phylogenetics, I: PROTML, maximum likelihood inference of protein phylogeny. (1992). Tokyo, Japan, Institute of Statistical Mathematics.

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

Developers

Per Kraulis

Categories

Structure Visualization

Versions

• Linux 32: 2.1.2
• Linux 64: 2.1.2
• OSX Intel: 2.1.2
• OSX PPC: 2.1.2
• SGI Irix: 2.1.2

Citations

Per J. Kraulis, "MOLSCRIPT: A Program to Produce Both Detailed and Schematic Plots of Protein Structures", Journal of Applied Crystallography (1991) vol 24, pp 946-950.

Technical Notes

OpenGL enable molscript is the default. The following aliases have been set to use a povray enabled version:

molscript-pov

molauto-pov

More information about the povray enabled version can be found here:

http://www.stanford.edu/~fenn/povscript/

• a package for processing film and image plate data.

Developers

Harry Powell

Categories

X-ray Crystallography

Versions

• Linux 32: 7.0.9
• Linux 64: 7.0.9
• OSX Intel: 7.0.9
• OSX PPC: 7.0.7
• SGI Irix: 6.2.5

Citations

Leslie. The integration of macromolecular diffraction data. Acta crystallographica Section D, Biological crystallography (2006) vol. 62 (Pt 1) pp. 48-57

Battye et al. iMOSFLM: a new graphical interface for diffraction-image processing with MOSFLM. Acta crystallographica Section D, Biological crystallography (2011) vol. 67 (Pt 4) pp. 271-81

Technical Notes

A graphical user interface to MOSFLM is provided by iMosflm.

• 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.

Developers

Jude Short

Categories

2D Crystallography

Electron Microscopy

Versions

• Linux 32: 05.05.2011
• Linux 64: 05.05.2011
• OSX Intel: 05.05.2011
• OSX PPC: 27.06.2007
• SGI Irix: 13.08.2002

Citations

Smith. Ximdisp--A visualization tool to aid structure determination from electron microscope images. Journal of structural biology (1999) vol. 125 (2-3) pp. 223-8

Crowther et al. MRC image processing programs. Journal of structural biology (1996) vol. 116 (1) pp. 9-16

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

Developers

Robert Edgar

Categories

Bioinformatics

Versions

• Linux 32: 3.8.31
• Linux 64: 3.8.31
• OSX Intel: 3.8.31
• OSX PPC: 3.8.31

Citations

Edgar. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic acids research (2004) vol. 32 (5) pp. 1792-7

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

Developers

Simon Hubbard

Categories

Structure Analysis

Versions

• Linux 32: 2.1.1
• Linux 64: 2.1.1
• OSX Intel: 2.1.1
• OSX PPC: 2.1.1

Citations

Hubbard, S.J. & Thornton, J.M. (1993), "NACCESS", Computer Program, Department of Biochemistry and Molecular Biology, University College London.

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

Developers

NAMD Developer Group

Categories

Computational Chemistry

Versions

• Linux 32: 2.9
• Linux 64: 2.9
• OSX Intel: 2.9
• OSX PPC: 2.7b3

Citations

Phillips et al. Scalable molecular dynamics with NAMD. Journal of computational chemistry (2005) vol. 26 (16) pp. 1781-802

• 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.

Developers

Mark Edel

NEdit Developers

Joachim Lous

Categories

Utilities

Versions

• Linux 32: 5.5
• Linux 64: 5.5
• OSX Intel: 5.5
• OSX PPC: 5.5

• 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.

Developers

Frank Delaglio

Ad Bax

Categories

NMR Methods

Versions

• Linux 32: 20130121
• Linux 64: 20130121
• OSX Intel: 20130121
• OSX PPC: 20110228
• SGI Irix: 2002

Citations

Delaglio et al. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. Journal of biomolecular NMR (1995) vol. 6 (3) pp. 277-93

Frank Delagio is no longer managing distribution or support. For distribution, licensing, permissions, email Ad Bax bax@nih.gov, for support contact Teddy Zartler at teddy@quantumtessera.com . To download the software: http://spin.niddk.nih.gov/NMRPipe/install/

Technical Notes

SBGrid has a site license that covers all participating laboratories.

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

Developers

Bruce Johnson

Categories

NMR Methods

Versions

• Linux 32: 8.0.3
• Linux 64: 8.0.3
• OSX Intel: 8.0.3
• OSX PPC: 8.0rc43

Citations

Bruce A. Johnson, Richard A. Blevins, NMR View: A computer program for the visualization and analysis of NMR data, Journal of Biomolecular NMR, Volume 4, Issue 5, Sep 1994, Pages 603 - 614. DOI 10.1007/BF00404272, URL http://dx.doi.org/10.1007/BF00404272

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

Developers

Luca Jovine

Categories

Structure Visualization

Nucleic Acids

Versions

• Linux 32: 1.5.2
• Linux 64: 1.5.2
• OSX Intel: 1.5.2
• OSX PPC: 1.5.2
• SGI Irix: 1.5

Citations

There is no paper describing nuccyl (yet). However, if you found the program useful and would like to mention it in your publications together with PyMOL, you could use an URL citation of the type:

Jovine, L. nuccyl (2003) http://www.biosci.ki.se/groups/ljo/software/nuccyl.html

• 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.

Developers

Roman Laskowski

Marina Santilli

Categories

Structure Analysis

Nucleic Acids

Versions

• Linux 32: 1.0
• Linux 64: 1.0
• OSX Intel: 1.0
• OSX PPC: 1.0
• SGI Irix: 1.0

Citations

Luscombe N M, Laskowski R A, Thornton J M. NUCPLOT: a program to generate schematic diagams of protein-DNA interactions. Nucleic Acids Research. 1997. 25:4940-4945.

• a model building application for X-ray crystallography.

Developers

Alwyn Jones

Categories

X-ray Crystallography

Versions

• Linux 32: 13.0
• Linux 64: 14.0.0
• OSX Intel: 14.0.0
• OSX PPC: 13.0
• SGI Irix: 10.0.1

Citations

Jones. Interactive electron-density map interpretation: from INTER to O. Acta crystallographica Section D, Biological crystallography (2004) vol. 60 (Pt 12 Pt 1) pp. 2115-25

Jones et al. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta crystallographica Section A, Foundations of crystallography (1991) vol. 47 ( Pt 2) pp. 110-9

Technical Notes

As of version 12.0, O no longer requires a license file.

To use custom O data files (rotamer database, interface files, etc), you must override the ODAT environmental variable to point to your own directory.

• Open a tcsh new shell and source /programs/labcshrc
• echo $ODAT (note the current O data directory
• cp -Rp $ODAT ~/o_data (copy the current O data files to your home directory)
• setenv ODAT ~/o_data (you can add this to your ~/.cshrc after the 'source /programs/labcshrc" line)

Copy your custom files to ~/o_data and then run your newly customized O.

O works with SGI Dials. If you're using OS X, you should download and install the most recent USB<->Serial adapter driver for dials use from David Gohara's website. The download file contains a PDF with instructions on installation and set up.

• 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.

Developers

Geoff Hutchison

Categories

Utilities

Versions

• Linux 32: 2.3.2
• Linux 64: 2.3.2
• OSX Intel: 2.3.2
• OSX PPC: 2.2.3

Citations

Guha et al. The Blue Obelisk -- Interoperability in Chemical Informatics. J. Chem. Inf. Model. 2006. 46(3) 991-998.

The Open Babel Package, version (xxx) http://openbabel.sourceforge.net/ (accessed Month Year)

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

Developers

RCSB

Categories

2D Crystallography

Utilities

Versions

• Linux 32: 8.120
• Linux 64: 8.120
• OSX Intel: 8.120
• OSX PPC: 8.061

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

Versions

• Linux 32: 5.10.1
• Linux 64: 5.10.1
• OSX Intel: 5.10.1
• OSX PPC: 5.10.1

• performs orientation searches and positional refinement of icosahedral viruses.

Developers

David Belnap

Categories

Electron Microscopy

Versions

• Linux 32: 20110124
• Linux 64: 20110124
• OSX Intel: 20110124
• OSX PPC: 20110124

Citations

PFT2: Baker and Cheng. A model-based approach for determining orientations of biological macromolecules imaged by cryoelectron microscopy. J Struct Biol. 1996. 116(1):120-30. Sanz-García et al. The random-model method enables ab initio 3D reconstruction of asymmetric particles and determination of particle symmetry. J Struct Biol. 2010. 171(2):216-22.

EM3DR2: Crowther et al. Three dimensional reconstructions of spherical viruses by fourier synthesis from electron micrographs. Nature. 1970. 226(5244):421-5.

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

Developers

Tim Pearson

Versions

• Linux 32: 5.2.2
• OSX Intel: 5.2.2
• OSX PPC: 5.2.2
• SGI Irix: 5.2.2

• (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.

Developers

Pavel Afonine

Ralf Grosse-Kunstleve

Nat Echols

Paul Adams

Categories

X-ray Crystallography

Versions

• Linux 32: 1.8.2-1309
• Linux 64: 1.8.2-1309
• OSX Intel: 1.8.2-1309
• OSX PPC: 1.7-650

Citations

Adams et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Cryst. 2010. D66: 213-221.

Technical Notes

If you use PHENIX to solve a structure please cite this publication:

PHENIX: building new software for automated crystallographic structure determination P.D. Adams, R.W. Grosse-Kunstleve, L.-W. Hung, T.R. Ioerger, A.J. McCoy, N.W. Moriarty, R.J. Read, J.C. Sacchettini, N.K. Sauter and T.C. Terwilliger. Acta Cryst. D58, 1948-1954 (2002)

• a free package of software programs for inferring phylogenies.

Developers

Joseph Felsenstein

Categories

Bioinformatics

Utilities

Versions

• Linux 32: 3.69
• Linux 64: 3.69
• OSX Intel: 3.69
• OSX PPC: 3.69

Citations

Felsenstein, J. 2005. PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle. or Felsenstein, J. 1989. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166.

• 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".

Developers

Ralf Glaser

Categories

Utilities

Versions

• Linux 32: 2.2
• Linux 64: 2.2
• OSX Intel: 2.2
• OSX PPC: 2.2

• 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.

Developers

Robert Maier

Versions

• Linux 32: 2.6
• Linux 64: 2.6
• OSX Intel: 2.6
• OSX PPC: 2.6

• (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.

Developers

POVRay Team

Categories

Utilities

Versions

• Linux 32: 3.6.1
• Linux 64: 3.6.1
• OSX Intel: 3.6
• OSX PPC: 3.6.1

• 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.

Developers

IVE Developer Group

Categories

Electron Microscopy

Tomography

Versions

• Linux 32: 4.2.7
• Linux 64: 4.2.7
• OSX Intel: 4.2.7
• OSX PPC: 4.2.7

Citations

Chen et al. IVE (Image Visualization Environment): a software platform for all three-dimensional microscopy applications. Journal of structural biology (1996) vol. 116 (1) pp. 56-60

Chen, H., Clyborne, W., Sedat, J.W., and Agard, D. A. (1992) PRIISM: an integrated system for display and analysis of three-dimensional microscope images. Proceedings of SPIE - the International Society for Optical Engineering. 1660: 784-790.

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

Developers

Steve Rozen

Categories

Bioinformatics

Versions

• Linux 32: 1.1.4
• Linux 64: 1.1.4
• OSX Intel: 1.1.4
• OSX PPC: 1.1.4

Citations

Koressaar and Remm. Enhancements and modifications of primer design program Primer3. Bioinformatics (Oxford, England) (2007) vol. 23 (10) pp. 1289-91

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

Categories

Bioinformatics

Versions

• Linux 32: 1.12
• Linux 64: 1.12
• OSX Intel: 1.12
• OSX PPC: 1.12

Citations

Do et al. ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome research (2005) vol. 15 (2) pp. 330-40

• 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.

Developers

Jane Richardson

David Richardson

Categories

Structure Analysis

Utilities

Versions

• Linux 32: 2.13.110830
• Linux 64: 2.13.110830
• OSX Intel: 2.13.110830
• OSX PPC: 2.12.071128

Citations

Word et al. Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. Journal of molecular biology (1999) vol. 285 (4) pp. 1711-33

Chen VB, Arendall WB III, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC (2010) "MolProbity: all-atom structure validation for macromolecular crystallography", Acta Crystallogr D66:12-21, open access, PMC2803126

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

Developers

Marina Santilli

Roman Laskowski

Categories

Structure Analysis

Versions

• Linux 32: 3.5.4
• Linux 64: 3.5.4
• OSX Intel: 3.5.4
• OSX PPC: 3.5.4
• SGI Irix: 3.5.4

Citations

Laskowski R A, MacArthur M W, Moss D S & Thornton J M (1993). PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst., 26, 283-291

• the ultimate protein least squares fitting program.

Developers

SciTech Software

Andrew Martin

Categories

Structure Analysis

Versions

• Linux 32: 3.1
• Linux 64: 3.1
• OSX Intel: 3.1
• OSX PPC: 3.1
• SGI Irix: 1.8

Citations

How to cite: Fitting was performed using the McLachlan algorithm (McLachlan, A.D., 1982. Rapid Comparison of Protein Structres, Acta Cryst A38, 871-873) as implemented in the program ProFit (Martin, A.C.R., http://www.bioinf.org.uk/software/profit/).

• a threading-based protein structure prediction system.

Developers

Kyle Ellrott

Ying Xu

Dong Xu

Rober Cottingham

Categories

Computational Chemistry

Versions

• Linux 32: 1.0
• Linux 64: 1.0
• OSX PPC: 2.0

Citations

Ying Xu and Dong Xu. Protein threading using PROSPECT: Design and evaluation. Proteins: Structure, Function, and Genetics. 40:343-354. 2000.

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

Developers

Marina Santilli

David Jones

Categories

Bioinformatics

Versions

• Linux 32: 3.2.1
• Linux 64: 3.2.1
• OSX Intel: 3.2.1
• OSX PPC: 3.2

Citations

McGuffin et al. The PSIPRED protein structure prediction server. Bioinformatics (Oxford, England) (2000) vol. 16 (4) pp. 404-5

• 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.

Categories

Structure Visualization

Versions

• Linux 32: 1.5.0.4
• Linux 64: 1.5.0.4
• OSX Intel: 1.5.0.4
• OSX PPC: 1.2r2
• SGI Irix: 0.99

Citations

The PyMOL Molecular Graphics System, Version 1.2r3pre, Schödinger, LLC.

Technical Notes

Pymol is installed with the APBS plugin. Your PDB must be in the following format:

1. No water or ligand molecules
2. B-factors < 100
3. No alternative conformations
4. No partial occupancies

• 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.

Developers

Sergey Lyskov,

Jeffrey Gray

PyRosetta Team

Categories

Computational Chemistry

Versions

• Linux 32: 2.0b
• Linux 64: 2.012
• OSX Intel: 2.0b
• OSX PPC: 1.1

Citations

Chaudhury et al. PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta. Bioinformatics (2010) vol. 26 (5) pp. 689-91

• 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.

Categories

Utilities

Versions

• Linux 32: 2.7
• Linux 64: 2.7.2
• OSX Intel: 2.7
• OSX PPC: 2.5.2

Citations

First publication, but quite outdated according to website: van Rossum and de Boer. Interactively Testing Remote Servers Using the Python Programming Language. CWI Quarterly. 1991. 4 (4):283-303.