Master List of Molecular Modeling Software

The following list of molecular modeling programs is provided for convenience and does not represent an endorsement of the providers or their products by the authors, the NIH or the U.S. Government.

Aarhus Univ.

Morten Kjeldgaard, Ph.D., Biostructural Chemistry, Dept. of Chemistry, Langelandsgade 140, DK-8000 Aarhus C, Denmark (+45 89 42 38 77 morten@oase.kemi.aau.dk).

"O"
- Platform(s): ESV, Silicon Graphics, HP.

American Chemical Society Software Div.

1155 Sixteenth St., NW, Washington, DC 20036 (202-872-4600).

ATOMLOGP
- Platform(s): PC.
NanoVision
- Platform(s): Macintosh.
- Version: 2.0.
PrologP and PrologD
- Platform(s): PC.

BioByte Corp.

Al Leo, Ph.D., P.O. Box 517, Claremont, CA 91711-0517 (909-621-8452; Fax: 909-624-5509).

Pomona College Models
- Platform(s): Silicon Graphics.

Biosym Technologies, Inc.

Headquarters: 9685 Scranton Road, San Diego, CA 92121 (619-458-9990).
Eastern Regional Office, 4 Century Drive, Parsippany, NJ 07054 (201-267-4476).

Apex
- Platform(s): Silicon Graphics.
Converter
- Platform(s): Silicon Graphics.
- Interface: Insight II.
Discover
- Platform(s): Cray, Silicon Graphics (R-4000, R-8000), SP2.
- Version: 2.9.5.
DMol
- Platform(s): Cray, Silicon Graphics (R-4000, R-8000), SP2.
- Version: 2.3.
DSPACE
- Platform(s): Silicon Graphics, VAX, SUN, Convex.
Homology
- Platform(s): Silicon Graphics.
- Interface: Insight II.
Insight II
- Platform(s): Silicon Graphics.
- Version: Insight II 2.30.
- Options:
  1. Sketch: Tools for drawing small molecules using the mouse.
  2. Delphi: Calculates, displays, and compares molecular electrostatic potentials.
  3. Biopolymer:Tools for building peptides and polynucleotides, and for editing proteins.
  4. Analysis: Tools for analyzing molecular dynamics trajectories calculated in Discover.
Ludi
- Platform(s): Silicon Graphics.
NMRchitect
- Platform(s): Silicon Graphics, IBM RS/6000.

Brookhaven National Laboratory

Chemistry Department, Bldg. 555, Upton, NY 11973 (516-282-3629 or pdb@bnl.gov).

Brookhaven Protein Databank
- Version: August, 1994.
- Platform(s): Convex, Macintosh.

CAChe Scientific, Inc.

18700 N.W. Walker Rd., Beaverton, OR 97006 (503-531-1800).

CAChe
- Platform(s): Server: IBM RS/6000, Silicon Graphics, PowerPC. Clients: Macintosh, PC, Silicon Graphics.

Cambridge Crystallographic Data Centre

Stephanie Hull, 12 Union Road, Cambridge CB2 1EZ, England (44-223-336408 or software@chemcrys.cam.ac.uk).

Cambridge Structural Database
Quest/Gstat (Search/Access Cambridge Structural Database)

Cambridge Scientific Computing, Inc.

Stuart Rubenstein, Ph.D., 875 Massachusetts Ave.,6th Floor, Cambridge, MA 02139 (617-491-2200).

Chem3D Plus
- Platform(s): Macintosh.
ChemDraw
- Platform(s): Macintosh.

Chemical Abstracts Service

2540 Olentangy River Road, Columbus, OH 43210 (800-753-4227).

CAS-3D
- Platform(s): Silicon Graphics.

Chemical Design, Inc.

US Sales Office: 200 Route 17 South, Ste. 120, Mahwah, NJ 07430 (201-529-3323).

ChemDBS-3D
- Platform(s): Silicon Graphics.
Chem-X
- Platform(s): Silicon Graphics.

Columbia University in the City of New York

Prof. Clark Still, Department of Chemistry, Havermeyer Hall, New York, NY 10027 (212-280-2577).

MacroModel
- Platform(s): Silicon Graphics (R-4000, R-8000), IBM RS/6000, SP2.
- Version: 4.5.

Columbia University in the City of New York

Anthony Nicholls, Ph.D., Department of Chemistry, Havermeyer Hall, New York, NY 10027 (nicholls@cuhhca.hhmi.columbia.edu).

Grasp
- Platform(s): Silicon Graphics.
- License required.

Cray Research

Cray Research Applications Department (1-800-289-CRAY or unichem@cray.com).

UniChem
- Platform(s): Silicon Graphics (client) and Cray supercomputer (server).

Duke University

David Richardson, Ph.D.

Kinemage (Mac) (PC)
- Platform(s): Macintosh, PC.

eduSoft, LC

P.O. Box 1811, Ashland, VA 23005.

HINT
- Interfaces: Chem-X (HINT 2.0C), Insight II (HINT 2.0I), or SYBYL (HINT 2.0S).
- Sales information available from David N. Haney, Ph.D., 12010 Medoc Lane, San Diego, CA 92131 (619-566-1127 or haney@netcom.com).

European Molecular Biology Laboratory (EMBL)

Uwe Hobohm, Ph.D., D-69012 Heidelberg, Germany (FAX: +49 6221 387 517 or sander@embl-heidelberg.de).

DSSP and related databases
- Platform(s): Unix.
- License required.
What If
- Platform(s): Silicon Graphics, ESV.
- Version: 4.0.
- License required.

Gaussian, Inc.

4415 Fifth Ave., Pittsburgh, PA 15213 (412-621-2050).

Gaussian
- Platform(s): Silicon Graphics (R-4000, R-8000), Convex, Cray.
- Version: 92.

Harvard Univ.

Martin Karplus, Ph.D., Dept. of Chemistry, 12 Oxford Street, Cambridge, MA 02138 (marci@tammy.harvard.edu).

CHARMM
- Platform(s): Unix.

Hypercube, Inc.

419 Phillip St., Waterloo, Ontario N2L 3X2 (519-725-4040).

HyperChem and ChemPlus
- Platform(s): PC.
HyperNMR
- Platform(s): PC.

IBM Corporation

Michel Dupuis, Ph.D., Neighborhood Road MLMA/428, Kingston, NY 12401 (914-385-4965).

HONDO
- Platform(s): SP2.
- Version: 8.4.

Iowa State Univ.

Mark Gordon, Ph.D., Dept. of Chemistry, Ames, IA 50011 (515-295-0425).

GAMESS (USA)
- Platform(s): Silicon Graphics (R-4000, R-8000), SP2.

Karolinska Institute

Per Kraulis, Ph.D., Center for Structural Biochemistry, Novum, S-141 57 Huddinge, SWEDEN (46 8 608 9266 or pjk@ciclid.csb.ki.se).

MolScript
- Platform(s): Silicon Graphics (should be portable to other Unix platforms).
- License required (send e-mail to the author, who will transfer the software by ftp).
- Comments: MolScript pictures can be greatly enhanced by Raster3D (see below). This is done by running MolScript with the "-r" flag to output a file that can be read by Raster3D.

Los Alamos National Laboratory

Chang-Shung Tung, Ph.D., MS k710, Los Alamos, NM 87545 (namot@transposon.lanl.gov).

NAMOT
- Platform(s): Silicon Graphics, Sun.
- Version: 2.0.

Ludwig Maximilians University

EGO
- Platform(s): Cray T3D, IBM SP1, workstation cluster (PVM), and Parsytec powerXplorer (PARIX).

Minnesota Supercomputer Center, Inc.

1200 Washington Avenue South, Minneapolis, MN 55415 (612-337-0200 or xmol@msc.edu).

XMol
- Platform(s): Unix.

Molecular Applications Group

445 Sherman Ave., Ste. T, Palo Alto, CA 94306 (415-473-3030).

MacImdad
- Platform(s): Macintosh (including Power Mac).

Molecular Design Ltd.

2132 Farallon Drive, San Leandro, CA 94577 (510-352-2870).

ISIS Base
- Platform(s): Macintosh, IBM PC 386 or 486.
ISIS Draw
- Platform(s): Macintosh, Silicon Graphics, PC.
ISIS Host
- Platform(s): IBM RS/6000.
- Interface: Works with ISIS Base.

Molecular Simulations, Inc.

Headquarters: 16 New England Executive Park, Burlington, MA 01803-5297 (617-229-9800).

CHARMm
- Platform(s): Convex, Silicon Graphics (R-4000, R-8000), SP2.
- Version: 22.
NMR Structure
- Platform(s): Silicon Graphics.
Polaris
- Platform(s): Silicon Graphics, IBM RS/6000, HP, ESV.
Protein Design
- Platform(s): Silicon Graphics, IBM RS/6000, DEC Alpha.
- Interface: QUANTA.
QUANTA
- Platform(s): Silicon Graphics, IBM RS/6000, DEC Alpha.
- Version: Quanta 4.0.
- Options:
  1. Protein Health: Tools for evaluating the quality of experimentally determined or modeled protein structures.
  2. Quantum Mechanics: Interface to MOPAC.
RECEPTOR
- Platform(s): Silicon Graphics.
XPLOR
- Platform(s): Silicon Graphics (R-4000, R-8000), SP2.
- Version: 3.1.

National Institutes of Health, DCRT, Laboratory of Structural Biology

Bernard Brooks, Ph.D., Division of Computer Research and Technology, Bldg. 12A/Room 2047, Bethesda, MD 20892 (301-496-0148 or brbrooks@helix.nih.gov). Copies of CHARMM are available through Harvard Univ.

CHARMM
- Platform(s): Convex, Cray, Hewlett-Packard, Intel.
- Version: 23.
CHARMM/GAMESS
- Platform(s): Hewlett-Packard.
Light/Light-Movie
- Platform(s): Hewlett-Packard, Apollo, Silicon Graphics.

National Institutes of Health, National Cancer Institute, Laboratory of Molecular Biology

B.K. Lee, Ph.D., Building 37/Room 4B15, Bethesda, MD 20892 (301-496-6580).

GEMM
- Platform(s): Silicon Graphics.

National Institutes of Health, National Cancer Institute, Division of Cancer Therapy

Dan Zaharevitz, Ph.D. (301-496-8747).

The Drug Information System 3D Database
- Platform(s): Silicon Graphics.
- Interface: Chem-X.

Oxford Molecular

700 East El Camino Real, Ste. Mountain View, CA 94040 (415-962-7300).

AbM (Antibody modeling)
- Platform(s): Silicon Graphics.
Anaconda
- Platform(s): Silicon Graphics.
Asp
- Platform(s): Silicon Graphics.
Cameleon
- Platform(s): Silicon Graphics.
Cobra
- Platform(s): Silicon Graphics.
Iditis
- Platform(s): Silicon Graphics.
Nemesis
- Platform(s): Silicon Graphics.
Tsar
- Platform(s): Silicon Graphics.
Vamp
- Platform(s): Silicon Graphics.

PSI International

Joe McDaniel, 810 Gleneagles Ct., Ste. 300, Baltimore, MD 21286 (410-821-5980).

Kekule
- Platform(s): Macintosh (requires ChemDraw, ISIS/Draw, or ChemIntosh), PC (self-contained).

Quantum Chemistry Program Exchange

Richard Counts, Ph.D., Creative Arts Building 181, Indiana University, Bloomington, IN 47405 (812-855-4784).

AMPAC (public domain version)
- Platform(s): Silicon Graphics, SP2.
- Interface: Insight II.
DGEOM (Dupont)
- Platform(s): Silicon Graphics, SP2, Adaptable to other platforms.
DGII
- Platform(s): Silicon Graphics.
GAMESS (public version)
- Platform(s): Convex, Cray.
MOPAC (Fujitsu)
- Platform(s): SUN (should be portable to other Unix platforms).
- Version: 93.
MOPAC (public version)
- Platform(s): SUN, SP2 (portable to other platforms).
- Version: 7.0.
MOPAC (public version)
- Platform(s): Convex, Silicon Graphics (R-4000, R-8000), Cray.
- Version: 6.0.
- Interface: Insight II, SYBYL, QUANTA.

Scripps Research Institute

Duncan McRee, Ph.D. (dem@scripps.edu).

XtalView

SemiChem

Andrew Holder, Ph.D., 7128 Summitt, Shawnee, KS 66216 (913-268-3271).

AMPAC
- Platform(s): Silicon Graphics (R-4000, R-8000), Convex, Cray, SUN, VAX, DEC Alpha.
- Version: 5.5.

SoftShell International

Craig Shelley, Ph.D., 715 Horizon Drive, Ste. 390, Grand Junction, CO 81506 (303-242-7502).

ChemIntosh II
- Platform(s): Macintosh.
ChemWindow
- Platform(s): PC.

Tripos Associates

Headquarters: 1699 South Hanley Road, Ste. 303, St. Louis, MO 63144 (800-323-2960).

Alchemy III
- Platform(s): Macintosh, PC.
CoMFA
- Platform(s): Silicon Graphics.
- Interface: SYBYL.
Composer
- Platform(s): Silicon Graphics, VAX, SUN, ESV, IBM RS/6000.
- Interface: SYBYL.
CONCORD
- Platform(s): Silicon Graphics.
- Interface: SYBYL.
DISCO
- Platform(s): Silicon Graphics.
- Interface: SYBYL.
LEAPFROG
- Platform(s): Silicon Graphics.
- Interface: SYBYL.
MatchMaker
- Platform(s): Silicon Graphics, VAX, SUN, ESV, IBM RS/6000.
PROTEP (Search Protein Databank)
- Platform(s): Silicon Graphics.
- Interface: SYBYL.
RECEPTOR
- Platform(s): Silicon Graphics.
- Interface: SYBYL.
SYBYL
- Platform(s): Silicon Graphics (R-4000), VAX, SUN, ESV, IBM RS/6000, Convex.
- Version: 6.1.
- Options:
  1. Advanced computation:Tools for performing conformational analysis; interface to MOPAC.
  2. QSAR: Tools for structure-activity analysis, including CoMFA, statistics, and comparisons.
  3. Dynamics: Performs molecular dynamics calculations and analysis.
  4. Biopolymer: Tools for building peptides and polynucleotides, and for editing proteins.
  5. Concord: Rapidly builds three-dimensional structures of organic molecules.
3DB UNITY
- Platform(s): Silicon Graphics.
- Interface: SYBYL.

University College, London

Ian McDonald, Ph.D., Biological Structure and Modelling Unit, Dept. of Biochemistry and Molecular Biology, Gower Street, London WC1E 6BT (mcdonald@bsm.bioc.ucl.ac.uk).

HBPlus
- Platform(s): Unix, VAX.
- Version: 3.0.
- License required.

University of Alabama

Mike Carson, Ph.D., Center for Macromolecular Crystallography (carson@gtx.cmc.uab.edu).

Ribbons
- Platform(s): Silicon Graphics.
- Version: 1.4.

University of Arizona

Pat Walters, Ph.D., Dolata Research Group, Department of Chemistry, Tucson, AZ 85721 (babel@mercury.aichem.arizona.edu).

Babel
- Platform(s): Unix.

University of Bayreuth

Prof. Dr. A. Kerber or Prof. Dr. R. Laue, Lehrstuhl II f. Mathematik, Universitat Bayreuth, 95440 Bayreuth, Germany (+49 (921) 553386 or molgen@btm2x2.mat.uni-bayreuth.de).

MOLGEN+
- Platform(s): PC.
- Version: 2.0.

University of California at San Francisco

Norma Belfer, Department of Pharmaceutical Chemistry, San Francisco, CA 94143 (415-476-5128).

Midas Plus
- Version: 2.0.
- License required.

University of California at San Francisco

Prof. Peter Kollman, Department of Pharmaceutical Chemistry S-1013, Third and Parnassus Ave., San Francisco, CA 94143 (415-476-1540).

AMBER (public version)
- Platform(s): Silicon Graphics (R-8000), Cray, SP2.
- Version: 4.0.
- License required.

University of California at San Francisco

Paul McCloskey, School of Pharmacy, Dept. of Pharmaceutical Chemistry, San Francisco, CA 94143-0446 (415-476-9031 or mcclosk@cgl.ucsf.edu).

Dock
- Platform(s): Silicon Graphics.

University of Edinburgh

Roger Sayle, Department of Computer Science, The King's Buildings, Mayfield Road, Edinburgh EH9 3JZ, Scotland (031 650 5163 or rasmol@dcs.ed.ac.uk).

RasMol /
- Platform(s): X-compatible Unix computers, Macintosh, PowerMac, and PCs running Microsoft Windows.
- Version: 2.4.

University of Florida

Rajiv Bendale, Ph.D., Quantum Theory Project, Department of Chemistry, Williamson Hall, Gainesville, FL 32611 (904-392-6711).

ZINDO
- Platform(s): Silicon Graphics.
- Version: 1988 release.
- Interface: SYBYL.

University of Illiois, Urbana-Champaign

Theoretical Biophysics Group, Beckman Institute for Advanced Science and Technology.

Visual Molecular Dynamics (VMD)
- Platform(s): Silicon Graphics.

University of Minnesota

Gopher (Search/Access Protein Databank)
- Platform(s): Macintosh, PC, All Unix Platforms.

University of Ottawa

Stephen V. Evans, Ph.D., Department of Biochemistry, Ottawa, Canada, K1H 8M5. (stephen.evans@nrc.ca).

Setor
- Platform(s): Silicon Graphics.
- Version: 4.13

University of Salzburg

Manfred J. Sippl, Ph.D., Center of Applied Molecular Engineering, Jakob-Haringer Str. 1, A-5020 Salzburg, Austria. (sippl@olga.came.sbg.ac.at).

PROSA II
- Platform(s): Silicon Graphics.
- License required.
- Version: 3.0

University of Washington

Ethan Merritt, Ph.D., Dept. of Biological Structure, SM-20, Seattle, Washington 98195 (merritt@u.washington.edu).

Raster3D: "Render", "Ribbon", and "Rods"

Wavefunction, Inc.

Warren Hehre, Ph.D., 18401 Von Karman, Ste. 370, Irvine, CA 92715 (714-955-2120).

Spartan
- Platform(s): Hewlett-Packard, IBM RS/6000, Silicon Graphics, SP2.
- Version: 3.1.

Yale University

F.M. Richards, Ph.D., Center for Structural Biology.

DEFINE_Structure (finds secondary structures in PDB files)
- Platform(s): Unix.