Programs for Protein, DNA, and RNA structure determination by NMR

Several groups at UC San Francisco have developped software useful for studying biomolecules with NMR. Software has been developped by Tom James' NMR group, Tack Kuntz's group, Peter Kollman's group, and the Computer Graphics Lab headed by Tom Ferrin. These programs and many others from other universities are listed below. Dates indicate when the program was last released as of Feb, 2000 with a few updated in June 2002.

*** indicates programs used at UC San Francisco

Processing

• Felix - 1998, processing and assignment, Molecular Simulations Inc.
• GIFA - Feb 1999, processing library
• * NMRPipe - Nov 1998, processing, Frank Delaglio, Ad Bax group, NIH
• VNMR - used with Varian spectrometers
• XWIN-NMR - used with Bruker spectrometers

Spectrum Display and Assignment

• ANSIG - Apr 1996, Per Kraulis, Upjohn Inc, Stockholm, free, F77, SGI
• Aurelia - 1999, graphical spectrum analysis, Peter Neideg, Bruker Inc.
• Felix - 1998, processing and assignment, Molecular Simulations Inc.
• NMRView - Jan 2000, graphical spectrum analysis, Bruce Johnson, Merck
• PIPP - contact Dan Garrett, NIH
• Pronto3D - Mar 1996, graphical spectrum analysis, Carlsberg Laboratory, Denmark
• * Sparky - Feb 2002, peak picking, assignment, integration for proteins + nucleic acids
• SPSCAN - Feb 2002, Ralf Glaser, peak picking, integration, analysis, free with source C++ code, Unix/X11
• TRIAD - Tripos graphical spectrum analysis package
• XEASY - Apr 1997, Ralf Glaser, ETH Zurich, $200, C, X/Motif

Automated resonance assignment

• AutoAssign - Nov 1999, protein backbone, free license, C++ server, Java interface, SGI, Linux, developped by Gaetano Montelione's group at Rutgers
• CONTRAST - Jan 1994, macros, text-based, free license, John B Olson's PhD work under John Markley, now Peter Lee. There is a commercial version which may be under development.
• GARANT - Jan 1998, free, uses homology with already assigned proteins, Peter Guntert, Kurt Wuthrich's group
• PASTA - May 1999, protein backbone, free, C with Tcl/Tk interface, SGI, source available, being worked on by Jens Liermann in Horst Kessler's group in Germany

Structure calculation

• * Amber - 1999, final structure refinement with best force field
• * ARIA - Jan 2000, automated noesy assignment and structure refinement with XPLOR
• * CORMA - June 1997, back calculate NOESY spectra using complete relaxation matrix method
• * DYANA - July 1998, NMR structure refinement using molecular dynamics in torsion angle space, $200 for academics
• * MARDIGRAS - June 1997, calculate distance restraints using complete relaxation matrix method
• MODELLER - June 1997, homology modelling, Andrej Sali, free
• MORASS - Dec 1998, calculate distance restraints or predict noesy intensities using relaxation matrix approach
• * XPLOR - 1996, structure refinement, X-ray and NMR, Axel Brunger's Lab

Molecule display

• Chime - Aug 1999, derived from RasMol, web browser plug-in, Windows and Mac only
• Cn3D - viewer for ASN.1 format models from NCBI Entrez, source code available
• * Chimera - surfaces, texture mapping, stereo, extendable
• GRASP - Dec 1994, SGI, $500 for academics or industry, Barry Honig's group
• * MidasPlus - Nov 1997, 3D display, stereo, Computer Graphics Lab, UCSF
• MolMol - May 1998, emphasis on NMR ensembles, publication quality images, free, Reto Koradi, Martin Billeter
• MolScript - Jan 1999, free for academics, source code, Per Kraulis
• O - May 99, Crystallographic macro molecular modelling package, Alwyn Jones, Morten Kjeldgaard
• RasMol - 1996, popular viewer for Windows, Mac, Unix.
• VMD - Jan 2000, molecular display, animation, Theoretical BioPhysics Group, UIUC

Other

• TALOS - 1999, prediction of protein phi and psi angles using a chemical shift database, Frank Delaglio, NIH

Shared display, teleconferencing, groupware

• CCF - Nov 1998, Collaborative Computing Frameworks for Natural Sciences Research, Emory University, SGI, Sun, Linux
• * VNC - Feb 2000, Remote desktop display, Unix, Windows, Mac
• xmx - June 1999, X Windows multiplexor, Solaris, Linux, HPUX, RS6000

Groups

• Tom Ferrin - Computer Graphics Lab, UCSF
• Thomas L James - UCSF
• Gaetano Montelione - Rutgers
• David Wemmer - Berkeley
• Kurt Wuthrich - ETH Zurich

Sites

• NMR Facility at Madison (NMRFAM)
• BioMagResBank
• NMR Information Server - University of Florida, lots on software, people, groups, ...
• NMRWeb - University of York, UK, software, people, meetings, ...
• Linux4Chemistry - lists NMR software for Linux
• LinuxNMR - Protein Structure Determination using Linux

Meetings

• Computational Aspects of Biomolecular NMR, Italy, June 6-11, 1999 (participants)