• 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.

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

Categories

Utilities

Versions

• Linux 32: 4.14
• Linux 64: 4.14
• OSX Intel: 4.14

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.

Developers

Automated Molecular Imaging Group

Bridget Carragher

Clint Potter

Versions

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

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.

Developers

David Soriano

Versions

• Linux 64: 2306

Citations

M. Harvey, G. Giupponi and G. De Fabritiis, ACEMD: Accelerating biomolecular dynamics in the microsecond time scale, J. Chem. Theory and Comput. 5, 1632 (2009).

M. J. Harvey and G. De Fabritiis, An implementation of the smooth particle-mesh Ewald (PME) method on GPU hardware, J. Chem. Theory Comput., 5, 2371–2377 (2009).

Buch I, Giorgino T and De Fabritiis G, Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations, PNAS (2011), 108, 10184-10189

• 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

• 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.

Developers

Geoff Barton

Categories

Bioinformatics

Versions

• Linux 32: 2.07a
• Linux 64: 2.07a
• SGI Irix: 2.07a

Citations

Barton. ALSCRIPT a tool to format multiple sequence alignments Protein Engineering. 1993. 6(1):37-40.

• the collective name for a suite of programs that allows users to carry out molecular dynamics simulations, particularly on biomolecules.

Amber was originally developed under the leadership of Peter Kollman. Current development stems from an active collaboration between David Case (Rutgers U), Tom Cheatham (U of Utah), Tom Darden (NIEHS, OpenEye, Ken Merz and Adrian Roitberg (Florida), Carlos Simmerling (SUNY-Stony Brook), Ray Luo (UC Irvine), Junmei Wang (UT Southwestern), and many others.

Developers

AMBER Admin

Nicole Flowers

Categories

Computational Chemistry

Versions

• Linux 32: various
• Linux 64: various
• OSX Intel: various

Citations

D.A. Case, T.A. Darden, T.E. Cheatham, III, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, R.C. Walker, W. Zhang, K.M. Merz, B. Roberts, B. Wang, S. Hayik, A. Roitberg, G. Seabra, I. Kolossvai, K.F. Wong, F. Paesani, J. Vanicek, J. Liu, X. Wu, S.R. Brozell, T. Steinbrecher, H. Gohlke, Q. Cai, X. Ye, J. Wang, M.-J. Hsieh, G. Cui, D.R. Roe, D.H. Mathews, M.G. Seetin, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A. Kovalenko, and P.A. Kollman (2010), AMBER 11, University of California, San Francisco.

Technical Notes

Please note that the Amber licensing agreement allows us to distribute the software only to Harvard-affiliated members. Labs without Harvard affiliation must purchase a separate license for Amber. Once you have acquired an Amber license, please contact us and we will add it to your installation.

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

Developers

Nicole A. Takesono Flowers

amber admin

Versions

• Linux 32: 1.5
• Linux 64: 1.5
• OSX Intel: 1.5

Technical Notes

If Amber is available at your site, the AmberTools installation bundled with the Amber installation with be configured and used in your shell. If your site does not have an Amber license, the standalone AmberTools installation will be configured in your shell.

If for some reason you want to use the standalone AmberTools instead of the version bundled with Amber, you can set AMBERTOOLS_PREFFERED=true in your ~/.sbgrid.conf to override the default setting.

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

Developers

Geoff Barton

Categories

Bioinformatics

Versions

• Linux 32: 2.3a
• Linux 64: 2.3a
• OSX Intel: 2.3a

Citations

Barton and Sternberg. Evaluation and Improvements in the Automatic Alignment of Protein Sequences. 1978a. Prot. Eng. 1:89-94.

Barton and Sternberg. A Strategy for the Rapid Multiple Alignment of Protein Sequences: Confidence Levels from Tertiary Structure Comparisons. J. Mol. Biol. 1978b. 198:327-337.

• 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.

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.

Developers

Clint Potter

Bridget Carragher

Automated Molecular Imaging Group

Versions

• Linux 64: 2.2
• OSX Intel: 2.2

• 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.

Developers

Jurgen Doreleijers

Categories

NMR Methods

Structure Analysis

Versions

• Linux 32: 3.2
• Linux 64: 3.2
• OSX Intel: 3.2
• SGI Irix: 3.2

Citations

Laskowski R.A., Rullmann J.A.C., MacArthur M.W., Kaptein R. & Thornton J.M. (1996). "AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR". J. Biomol. NMR 8, 477-486.

Doreleijers J.F., Rullmann J.A.C. & Kaptein R. (1998). "Quality assessment of NMR structures: a statistical survey". J. Mol. Biol. (1998) 281:149-164.

Doreleijers J.F., Raves M.L., Rullmann J.A.C. & Kaptein R. (1999). "Completeness of NOEs in proteins, a statistical analysis of NMR data". J. Biomol. NMR (1999) 14, 123-132.

• (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.

Developers

Benjamin Bardiaux

Therese Malliavin

Categories

NMR Methods

Versions

• Linux 32: 2.3.1
• Linux 64: 2.3.1
• OSX Intel: 2.3.1

Citations

Rieping et al. ARIA2: automated NOE assignment and data integration in NMR structure calculation. Bioinformatics (2007) vol. 23 (3) pp. 381-2

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

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.

Developers

Geoff Hutchison

Versions

• Linux 32: 1.1.0
• Linux 64: 1.1.0
• OSX Intel: 1.1.0

Citations

The preferred way to cite Avogadro is: Avogadro: an open-source molecular builder and visualization tool. Version 1.XX. http://avogadro.openmolecules.net/

Marcus D Hanwell, Donald E Curtis, David C Lonie, Tim Vandermeersch, Eva Zurek and Geoffrey R Hutchison; "Avogadro: An advanced semantic chemical editor, visualization, and analysis platform" Journal of Cheminformatics 2012, 4:17.

• 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

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

Developers

Niko Grigorieff

Versions

• Linux 32: 1.04
• Linux 64: 1.04
• OSX Intel: 1.04

• 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.

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

Versions

• Linux 32: 2.2.25
• Linux 64: 2.2.25
• OSX Intel: 2.2.25

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

Developers

Dave Knoester

Jeffrey Barrick

Categories

Bioinformatics

Versions

• Linux 32: 1.00rc8
• Linux 64: 1.00rc8
• OSX Intel: 1.00rc8

• 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

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

Developers

Niels Volkmann

Categories

Electron Microscopy

Versions

• Linux 32: 20.1
• Linux 64: 20.2
• OSX Intel: 20.1

Citations

Owen et al. Image analysis of helical objects: the Brandeis Helical Package. J Struct Biol (1996) vol. 116 (1) pp. 167-75

• 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

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.

Developers

Jiří Damborský

Versions

• Linux 32: 3.0
• Linux 64: 3.0
• OSX Intel: 3.0

Citations

Eva Chovancová, Antonín Pavelka, Petr Beneš, Ondřej Strnad, Jan Brezovský, Barbora Kozlíková, Artur Gora, Vilém Šustr, Martin Klvaňa, Petr Medek, Lada Biedermannová, Jiří Sochor & Jiří Damborský: CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures, PLoS Computational Biology 8: e1002708, 2012.

• (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

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.

Developers

Magnus Lundborg

Tim Stevens

Versions

• Linux 32: 0.6.1
• Linux 64: 0.6.1
• OSX Intel: 0.6.1

Technical Notes

The currently available version is a beta test release and bug reports are welcome. Bug reports should be made via the CCPNMR mailing list at JISC.

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

Developers

Michael Lappe

Categories

Structure Analysis

Structure Visualization

Versions

• Linux 32: 1.1rc6
• Linux 64: 1.1rc6
• OSX Intel: 1.1rc6

Citations

Vehlow et al. CMView: interactive contact map visualization and analysis. Bioinformatics (2011) vol. 27 (11) pp. 1573-4

• 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

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

Versions

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

Technical Notes

Reference to cite: G. Jogl, X. Tao, Y. Xu & L. Tong. (2001). COMO: A program for combined molecular replacement. Acta Cryst. D57, 1127-1134.

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

Developers

Bert de Groot

Categories

Computational Chemistry

Versions

• Linux 32: 2.1.2
• Linux 64: 2.1.2
• OSX Intel: 2.1.2

Citations

de Groot et al. Prediction of protein conformational freedom from distance constraints. Proteins (1997) vol. 29 (2) pp. 240-51

• (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.

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

Developers

Arthur Palmer

Categories

NMR Methods

Versions

• Linux 32: 1.43
• Linux 64: 1.43
• OSX Intel: 1.43

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

Developers

Niko Grigorieff

Versions

• Linux 32: 20120305
• Linux 64: 20120305
• OSX Intel: 20120305

• (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.

Developers

Ad Bax

Categories

NMR Methods

Versions

• Linux 32: 1.02
• Linux 64: 20120910
• OSX Intel: 20120910

Citations

Shen et al. De novo protein structure generation from incomplete chemical shift assignments. J Biomol NMR (2009) vol. 43 (2) pp. 63-78

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.

Developers

Niko Grigorieff

Versions

• Linux 32: 20120506
• Linux 64: 20120506
• OSX Intel: 20120506

Citations

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

• 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 the automated structure calculation of biological macromolecules on the basis of conformational constraints from NMR.

Developers

L.A.Systems, Inc.

Peter Güntert

Categories

NMR Methods

Versions

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

Citations

Güntert. Automated NMR structure calculation with CYANA. Methods Mol Biol (2004) vol. 278 pp. 353-78

Technical Notes

CYANA is commercial software and is licensed on a per-lab basis. Once you have purchased a license, please contact us to let us know, and we will be able to remotely install the software for your lab.

• a software suite and toolkit that processes single crystal X-ray diffraction images from two-dimensional position sensitive detectors.

Categories

X-ray Crystallography

Versions

• Linux 32: various
• Linux 64: 9.9.9.6
• OSX Intel: various

Citations

Pflugrath. The finer things in X-ray diffraction data collection. Acta Crystallogr D Biol Crystallogr (1999) vol. 55 (Pt 10) pp. 1718-25

Technical Notes

We can provide updated d*TREK binaries for your installation, but this software requires an individual license for each lab. Please contact license-request@Rigaku.com to procure a license.

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

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.

Developers

Niko Grigorieff

Versions

• Linux 32: 20120330
• Linux 64: 20120330
• OSX Intel: 20120330

• 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

Particle picker that uses difference of Gaussians (DoG) for picking particles.

Developers

Automated Molecular Imaging Group

Versions

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

• 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.

Developers

Jan Hermans

Categories

Structure Analysis

Versions

• Linux 32: 200304
• Linux 64: 200304
• OSX Intel: 200304

• (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.

Developers

Marian Szebenyi

Categories

X-ray Crystallography

Versions

• Linux 32: 2.13
• Linux 64: 2.13

Citations

Rossmann and van Beek. Data processing. Acta Crystallogr D Biol Crystallogr (1999) vol. 55 (Pt 10) pp. 1631-40

• 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 program for NMR structure calculation based on a highly efficient implementation of torsion angle dynamics. It is the successor of DIANA, the first program package for NMR structure calculation developed by P. Güntert. DYANA is no longer available or supported. Its functionality has been incorporated into the program package CYANA.

Developers

Peter Guentert

Categories

NMR Methods

Versions

• Linux 32: 1.5
• Linux 64: 1.5
• OSX Intel: 1.5

Citations

Güntert et al. Torsion angle dynamics for NMR structure calculation with the new program DYANA. J Mol Biol (1997) vol. 273 (1) pp. 283-98

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.

Developers

Daniel Castaño-Diez

Versions

• Linux 64: 1.0.14
• OSX Intel: 1.0.14

Citations

Castaño-Díez D, Kudryashev M, Arheit M, Stahlberg H., J Struct Biol. 2012 Jan 8.

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

Developers

Steven Hayward

Categories

Structure Analysis

Versions

• Linux 32: 1.02
• Linux 64: 1.02
• OSX Intel: 1.02

Citations

Hayward and Lee. Improvements in the analysis of domain motions in proteins from conformational change: DynDom version 1.50. J Mol Graph Model (2002) vol. 21 (3) pp. 181-3

• 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

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

Developers

Hanna Szoke

Categories

X-ray Crystallography

Versions

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

Citations

Murray et al. Capture and visualization of a catalytic RNA enzyme-product complex using crystal lattice trapping and X-ray holographic reconstruction. Mol Cell (2000) vol. 5 (2) pp. 279-87

• (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

• (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.

Developers

David Stokes

Versions

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

• 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.

Developers

Jose-Jesus Fernandez

Categories

Electron Microscopy

Versions

• Linux 32: 200912
• Linux 64: 200912
• OSX Intel: 200912

Citations

Fernández et al. Sharpening high resolution information in single particle electron cryomicroscopy. Journal of structural biology (2008) vol. 164 (1) pp. 170-5

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

Developers

Michael Schatz

Categories

Electron Microscopy

Versions

• Linux 32: 090720
• Linux 64: 090720
• OSX Intel: 090720

• 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 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.

Developers

Charles Kissinger

Categories

X-ray Crystallography

Versions

• Linux 32: 11.02
• Linux 64: 11.02
• OSX Intel: 11.02
• SGI Irix: 3.1

Citations

Kissinger et al. Rapid automated molecular replacement by evolutionary search. Acta crystallographica Section D, Biological crystallography (1999) vol. 55 (Pt 2) pp. 484-91

• 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.

Developers

Thomas Schneider

Categories

Structure Analysis

Versions

• Linux 32: 0.7i
• Linux 64: 0.7i

Citations

Schneider. Domain identification by iterative analysis of error-scaled difference distance matrices. Acta crystallographica Section D, Biological crystallography (2004) vol. 60 (Pt 12 Pt 1) pp. 2269-75

Schneider. A genetic algorithm for the identification of conformationally invariant regions in protein molecules. Acta crystallographica Section D, Biological crystallography (2002) vol. 58 (Pt 2) pp. 195-208

Schneider. Objective comparison of protein structures: error-scaled difference distance matrices. Acta crystallographica Section D, Biological crystallography (2000) vol. 56 (Pt 6) pp. 714-21

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

Developers

Espript Info

Xavier ROBERT

Categories

Structure Analysis

Structure Visualization

Versions

• Linux 32: 2.3
• Linux 64: 2.3
• OSX Intel: 2.3

Citations

Gouet et al. ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins. Nucleic acids research (2003) vol. 31 (13) pp. 3320-3

Gouet et al. ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics (Oxford, England) (1999) vol. 15 (4) pp. 305-8

• 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

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.

Developers

Pierre Tuffery

fpocket support

Versions

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

• (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

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

Developers

Brian Osher

Scott Smith

Versions

• Linux 32: 4.3.2
• Linux 64: 4.3.2
• OSX Intel: 4.3.2

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).

Developers

Yifan Cheng

Versions

• Linux 64: 8.06-20110514

Citations

http://dx.doi.org/10.1016/j.jsb.2010.06.010

Technical Notes

1) At least two NVIDIA GPUs (required by the reconstruction). NVIDIA GeForce GTX295 or better is recommended.

2) It is strongly recommended that the graphic card used GPU computing by FREALIGN does not connect to any monitor. CUDA has a 5 sec executing time limit and the GPU connected to a monitor may be unstable.

3) The box size of particle images should be smaller than 500 pixels.

4) The original FREALIGN integrates both alignment and reconstruction into a single executable file. In the current GPU version of FREALIGN, the two functions are separated and compiled into two separate executable files. The source codes are kept in two separate folders: src_ref and src_rec. Otherwise, the usage of the GPU-enabled FREALIGN is exactly same as the original FREALIGN.

5) Because the multithread processing has been embedded, a single FREALIGN process will occupy all the available GPU resources in one computer. So each computer or cluster node can run only one FREALIGN job.

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

Developers

Roman Laskowski

Marina Santilli

Categories

Structure Analysis

Versions

• Linux 32: 3.15
• Linux 64: 3.15
• OSX Intel: 3.15

Citations

McDonald and Thornton. Satisfying hydrogen bonding potential in proteins. Journal of molecular biology (1994) vol. 238 (5) pp. 777-93

• 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 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.

Developers

Mark Sansom

Oliver Smart

Categories

Structure Analysis

Versions

• Linux 32: 2.1-b3
• Linux 64: 2.11

Citations

Smart et al. HOLE: a program for the analysis of the pore dimensions of ion channel structural models. Journal of molecular graphics. 1996. 14 (6): 354-60, 376.

Technical Notes

The hole program is now hosted by the Sansom Laboratory at the University of Oxford.

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.

Versions

• Linux 32: 7c
• Linux 64: 7c

Citations

García de la Torre J, Huertas ML, Carrasco B. HYDRONMR: prediction of NMR relaxation of globular proteins from atomic-level structures and hydrodynamic calculations. J Magn Reson. 2000 Nov;147(1):138-46.

• a subset of chemical compounds that are used for screening at the ICCB-Longwood Screening Facility. The dataset was compiled by David Wrobel (ICCB-Longwood) for in silico docking. The date-stamped datasets are available in /programs/share/iccb.

Developers

David Wrobel

Categories

Computational Chemistry

Versions

• 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.

Developers

Team ilastik

Versions

• Linux 64: 0.5.04
• OSX Intel: 0.5.06

Citations

C. Sommer, C. Straehle, U. Köthe, and F.A. Hamprecht 8th IEEE International Symposium on Biomedical Imaging (ISBI 2011), in press

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.

Categories

Electron Microscopy

Utilities

Versions

• Linux 32: fiji
• Linux 64: fiji
• OSX Intel: fiji

• 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

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

Developers

Andrej Sali

Ben Webb

Categories

Computational Chemistry

Versions

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

Citations

D. Russel, K. Lasker, B. Webb, D. Schneidman, J. Velázquez-Muriel, A. Sali, "Putting the pieces together: integrative structure determination of macromolecular assemblies", PLoS Biology, 2012.

Webb B, Lasker K, Schneidman-Duhovny D, Tjioe E, Phillips J, Kim SJ, Velázquez-Muriel J, Russel D, Sali A. Modeling of proteins and their assemblies with the integrative modeling platform. Methods Mol Biol. 2011;781:377-97.

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

Developers

sven hyberts

gerhard wagner

Versions

• Linux 32: 20130212
• Linux 64: 20130212
• OSX Intel: 20130212

Technical Notes

istHMS: IST reconstructions are performed by manipulating the conventional work-flow for fourier transform of regular NMR data with NMRPipe. Data is converted and transformed in the direct dimension in much the same way as regular NMRPipe. Before transform in non-uniform dimensions, the IST procedure must be applied. To do this, several scripts along with the IST software have been devised. schedule generator: At the core of Non Uniform Sampling and reconstructing of the resultant spectra is selecting which points to acquire and which to skip. Work in our lab has established the Poisson Gap Sampling Method (Hyberts et al, JACS, 2010) results in superior schedules with fewer artifacts during Forward Maximum Entropy reconstruction. Empirical evidence from our lab (unpublished) suggests this is also true for the Iterative Soft Threshold algorithm. You can create your own schedules using our Poisson Gap Schedule Java applet.

• 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

• (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.

Developers

Lafire Developer Group

M Yao

Categories

X-ray Crystallography

Versions

• Linux 32: 3.5
• Linux 64: 3.5
• OSX Intel: 3.5

Citations

Yao et al. LAFIRE: software for automating the refinement process of protein-structure analysis. Acta Crystallogr D Biol Crystallogr (2006) vol. 62 (Pt 2) pp. 189-96

• 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 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.

Developers

Marina Santilli

Roman Laskowski

Categories

Structure Analysis

Versions

• Linux 32: 1.42
• Linux 64: 1.42
• OSX Intel: 1.42

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