• 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.

• 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.

• 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.

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

• 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

• (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

• 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

• 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.

• 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 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 model building application for X-ray crystallography.

Developers

Dusan Turk

Categories

X-ray Crystallography

Versions

• Linux 32: 2011
• Linux 64: 2011
• OSX Intel: 2011
• SGI Irix: 2004

Citations

D.Turk: "MAIN 96: An interactive software for density modifications, model building, structure refinement and analysis." Proceedings from the 1996 meeting of the International Union of Crystallography Macromolecular Macromolecular Computing School, eds

• 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

• 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.

• 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 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

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

Developers

Markus Zweckstetter

Categories

NMR Methods

Versions

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

Citations

Zweckstetter. NMR: prediction of molecular alignment from structure using the PALES software. Nature protocols (2008) vol. 3 (4) pp. 679-90

Zweckstetter et al. Prediction of charge-induced molecular alignment of biomolecules dissolved in dilute liquid-crystalline phases. Biophysical journal (2004) vol. 86 (6) pp. 3444-60

• 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/).

• 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

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

Developers

Ethan Merritt

Categories

Structure Visualization

Versions

• Linux 32: 3.0
• Linux 64: 3.0
• OSX Intel: 3.0
• OSX PPC: 2.7d
• SGI Irix: 2.6e

Citations

Merritt and Bacon. Raster3D: photorealistic molecular graphics. Meth Enzymol (1997) vol. 277 pp. 505-24

Merritt and Murphy. Raster3D Version 2.0. A program for photorealistic molecular graphics. Acta Crystallogr D Biol Crystallogr (1994) vol. 50 (Pt 6) pp. 869-73

• a suite of programs for molecular replacement calculations. It currently consists of two major programs, GLRF for rotation function calculations and TF for translation function calculations. In addition, a small program (ANGCAL) is a convenient tool for conversions between angles and matrices.

Developers

Liang Tong

Categories

X-ray Crystallography

Versions

• Linux 32: 4.1
• Linux 64: 4.1
• OSX Intel: 4.1
• OSX PPC: 4.1
• SGI Irix: 4.1

Citations

Tong and Rossmann. Rotation function calculations with GLRF program. Meth Enzymol (1997) vol. 276 pp. 594-611

• a popular molecular graphics software display package.

Developers

Mike Carson

Categories

Structure Visualization

Versions

• Linux 32: 3.32
• Linux 64: 3.32
• OSX Intel: 3.5
• OSX PPC: 3.5
• SGI Irix: 3.2

Citations

Carson. Ribbons. Meth Enzymol (1997) vol. 277 pp. 493-505

Technical Notes

Ribbons is supported on Fedora Core releases 3 and lower and Fedora releases 7 and higher. Due to significant library compatibility issues, ribbons is not supported on Fedora Core 4 through 6.

• a suite of programs for sequence alignment including: aln, swg, prrn, phyln and makmdm.

aln: Pairwise alignment of biological sequences supporting spliced alignment procedures.

swg: locally aligns a pair of DNA or protein sequences by Smith-Waterman-Gotoh algorithm. Currently spliced alignment is not supported. Profile version is very slow.

prrn: global multiple alignment of a set of protein or DNA sequences by doubly nested iterative refinement method.

phyln: UPGMA or NJ method to make a phylogenetic tree from a multiple alignment.

makmdm: constructs binary PAM matrices. Must be run once before the first run of aln, swg or prrn.

Developers

Oasmu Gotoh

Categories

Bioinformatics

Versions

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

• a set of programs for macromolecular phasing. SHELXC is designed to provide a simple and fast way of setting up the files for the programs SHELXD (heavy atom location) and SHELXE (phasing and density modification) for macromolecular phasing by the MAD, SAD, SIR and SIRAS methods. hkl2map provides a simple user interface to SHELX and is installed separately. SHELX was written and is actively maintained by George Sheldrick and his group at the University of Gottingen.

All users must first obtain license from George Sheldrick, and then request software installation by writing to bugs@sbgrid.org.

Developers

George Sheldrick

Categories

X-ray Crystallography

Versions

• Linux 32: 97-2.20090720
• Linux 64: 97-2
• OSX Intel: 97-2.20090720
• OSX PPC: 97-2.20090720
• SGI Irix: 97-2

Citations

Sheldrick. A short history of SHELX. Acta Cryst. 2008. A64:112-122.

Technical Notes

All users must first obtain license from George Sheldrick, and then request software installation by writing to bugs@sbgrid.org.

• a program package for modeling of atomic resolution structures into low-resolution density maps. The software supports both rigid-body and flexible docking using a variety of fitting strategies.

Developers

Situs Developer Team

Willy Wriggers

Categories

Electron Microscopy

SAXS

Versions

• Linux 32: 2.6.3
• Linux 64: 2.6.3
• OSX Intel: 2.6.3
• OSX PPC: 2.6.1
• SGI Irix: 2.1a3

Citations

Wriggers. Using Situs for the Integration of Multi-Resolution Structures. Biophysical Reviews. 2010. 2: 21-27.

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

Developers

Tom Terwilliger

Categories

X-ray Crystallography

Versions

• Linux 32: 2.13
• Linux 64: 2.13
• OSX Intel: 2.13
• OSX PPC: 2.13
• SGI Irix: 2.10

Citations

SOLVE: Terwilliger and Berendzen. Automated MAD and MIR structure solution. Acta Crystallographica. 1999. D55:849-861.

RESOLVE: Terwilliger. Maximum likelihood density modification. Acta Cryst. 2000. D56:965-972.

RESOLVE model-building: Terwilliger. Automated main-chain model building by template matching and iterative fragment extension. Acta. Cryst. 2003. D59:38-44.

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

Developers

ArDean Leith

Joachim Frank

Categories

Electron Microscopy

Versions

• Linux 32: 20.12
• Linux 64: 20.12
• OSX Intel: 20.12
• OSX PPC: 13.0
• SGI Irix: 8.02

Citations

Frank et al. SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. J Struct Biol. 1996. 116(1):190-9.

Technical Notes

Start the vncserver & vncviewer

vncserver :5 -cc 3 -depth 8 -localhost -geometry 1252x934
vncviewer :5

When the viewer window closes, the vncserver will be killed

vncserver -kill :5
to reset password remove .vnc directory from your HOME

The OSX build is a test build of the port. If there are any problems please
let us know so that we can correct them immediately.

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

Developers

Geoff Barton

Categories

Structure Analysis

Versions

• Linux 32: 4.4
• Linux 64: 4.4
• OSX Intel: 4.4
• OSX PPC: 4.4
• SGI Irix: 4.2

Citations

Russell & Barton. Multiple protein sequence alignment from tertiary structure comparison, PROTEINS: Struct. Funct. Genet. 1992. 14: 309-323.

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

Developers

Marina Santilli

Roman Laskowski

Categories

Structure Analysis

Versions

• Linux 32: 1.4.2
• Linux 64: 1.4.2
• OSX Intel: 1.4.2
• OSX PPC: 1.4.2
• SGI Irix: 1.4.2

Citations

Confidentiality agreement is signed and redistribution to member laboratories is fine. There is no need to send a list of users.

Laskowski. SURFNET: A program for visualizing molecular surfaces, cavities and intermolecular interactions. J. Mol. Graph. 1995. 13: 323-330.

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

Developers

Nicolas Guex

Torsten Schwede

Categories

Structure Analysis

Versions

• Linux 32: 3.7sp5
• Linux 64: 3.7sp5
• OSX Intel: 4.1.0
• OSX PPC: 4.0
• SGI Irix: 3.7

Citations

Guex and Peitsch.SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis. 1997. 18:2714-2723.

• offers protein fold recognition by optimal protein sequence threading.

Developers

David Jones

Categories

Computational Chemistry

Versions

• Linux 32: 3.5
• Linux 64: 3.5
• SGI Irix: 3.5

Citations

Jones et al. A new approach to protein fold recognition. Nature. 1992. 358: 86-89.

Jones et al. Successful protein fold recognition by optimal sequence threading validated by rigorous blind testing. Proteins. 1995. 23: 387-397.

Jones. THREADER : Protein Sequence Threading by Double Dynamic Programming. (in) Computational Methods in Molecular Biology. Steven Salzberg, David Searls, and Simon Kasif, Eds. Elsevier Science. 1998. Chapter 13.

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

Developers

Borries Demeler

Categories

Utilities

Versions

• Linux 32: 9.9-1497
• Linux 64: 9.9-1497
• OSX Intel: 9.9-1504
• OSX PPC: 7.0
• SGI Irix: 5.0

Citations

Demeler et al. Characterization of reversible associations by sedimentation velocity with UltraScan. Macromol Biosci. 2010. 10(7):775-82.

Demeler et al. Analysis of heterogeneity in molecular weight and shape by analytical ultracentrifugation using parallel distributed computing. Methods Enzymol. 2009. 454:87-113.

Technical Notes

Each user has to register separately and then place the license file in their home directory. Ultrascan License Request

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

Developers

VMD Developer Team

Categories

Structure Visualization

Versions

• Linux 32: 1.9.1
• Linux 64: 1.9.1
• OSX Intel: 1.9.1
• OSX PPC: 1.8.7
• SGI Irix: 1.7.1

Citations

Humphrey et al. VMD - Visual Molecular Dynamics. J. Molec. Graphics. 1996. 14: 33-38. For a list of other citations go to: http://www.ks.uiuc.edu/Research/vmd/allversions/citations/

Technical Notes

Condensed “movie making tips” from VMD. The main points:

1. Just load 1 frame for every 1ns of simulation time. A 1 us simulation would only need 1000 frames. The “stride” feature in the VMD trajectory loader dialog lets you set this (e.g. to 20, if the generated frames are at a rate of 50 ps per frame). Make sure you choose “load all frames at once”, rather than “background”. The “background” option will render frames as they’re loaded.

2. Figure out what region you want to “fix” in the structure. Get the residue IDs for this. Go to Extensions→Analysis→RMSD Tool and enter “protein and resid START to STOP”, then click on “Align”. This will align the entire structure through all frames and have resids START to STOP as stationary as possible.

3. Use “Create Rep” to create multiple representations of the structure. The selection box can be used to specify what you want to show. “protein and resid START1 to STOP1 START2 to STOP2 …” is a common entry. “water and within 3 of protein” would show all water molecules within 3A of an atom associated with a protein. You can then play with the different kinds of views (coloring, style, transparency) for each representation individually.

4. Clicking on a representation will show or hide it.

5. For each representation, set the Trajectory to smooth over several frames. I have found that a 4ns smoothing window reduces the jitter without eliminating interesting side chain motion. YMMV.

6. Set Display→Rendermode→GLSL to do OpenGL/CUDA rendering. This should make a big difference. I haven't done a formal test of this, but my laptop, with 48 CUDA 3 processing cores, seems to do much better, smoother, and faster rendering than my Mac Pro (which does not have a compatible CUDA card).

Movie Making:

• loaded every 20th frame (about 1000 from 20k) * smoothing window of 4  * internal Tachyon ray tracer  * image smoothing on  * half size reduction * 30 FPS (NTSC) * MPEG output

Apparently a good trick to get nice looking animations is to double therendering window then set the movie generator to half-size the result. I guess this gives a “per-frame” image smoothing effect as thepotentially hard edged rendered image is reduced to an anti-aliased frame.

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

Developers

Gert Vriend

Categories

Structure Analysis

Versions

• Linux 32: 10.1.1
• Linux 64: 10.1.1
• OSX Intel: 8.0
• OSX PPC: 20030601-1154
• SGI Irix: 19970704-1848

Citations

Hooft et al. Errors in protein structures. Nature. 1996. 381: 272.

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

Developers

Wolfgang Kabsch

Categories

X-ray Crystallography

Versions

• Linux 32: 20120926
• Linux 64: 20120926
• OSX Intel: 20120926
• SGI Irix: December-2004

Citations

Kabsch. XDS. Acta Cryst. 2010. D66: 125-132. Additional references found at http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/references.html

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

Developers

Sharron Thomas

Kurt Wuthrich

Categories

NMR Methods

Versions

• Linux 32: 1.2
• Linux 64: 1.2
• SGI Irix: 1.2

Citations

Bartels C et al. The program XEASY for computer-supported NMR spectral analysis of biological macromolecules. J. Biomol. NMR. 1995. 6: 1–10.

Technical Notes

Start the vncserver & vncviewer

vncserver :5 -cc 3 -depth 8 -localhost -geometry 1252x934
vncviewer :5

When the viewer window closes, the vncserver will be killed

vncserver -kill :5
to reset password remove .vnc directory from your HOME

• a system for X-ray crystallography and NMR.

Developers

Charles Schwieters

Categories

NMR Methods

Versions

• Linux 32: 2.33
• Linux 64: 2.33
• OSX Intel: 2.33
• OSX PPC: 2.27
• SGI Irix: 3.851

Citations

Schwieters CD et al. The Xplor-NIH NMR Molecular Structure Determination Package. J. Magn. Res. 2003. 160: 66-74.

Schwieters CD. Using Xplor-NIH for NMR molecular structure determination. Progr. NMR Spectroscopy. 2006. 48: 47-62.