This document contains a set of indexes to the master software list.

Custom Lists
  1. Software Suppliers
  2. Software Available at NIH
  3. Software With Associated WWW Sites
  4. Software With Available Electronic Documentation

Software Indexed by Implementation

  1. Multi-Purpose Packages
  2. Personal Computer-Based Packages

Software Indexed by Functionality

  1. Chemical Structure Drawing Packages
  2. Utilities
  3. Structure Databases
  4. Model Building
  5. Computation Engines
  6. Geometry Engines
  7. Graphics Engines

Software Indexed by Application Area

  1. Biopolymers
  2. Structure-Activity
  3. Docking/Structure-Based Drug Design

Software Available at NIH

Please note the following: Further information about accessing software on NIH computers is available elsewhere.
  1. AMBER (public version dist. by UCSF)
    1. Frederick Biomedical Supercomputing Center.
  2. Brookhaven Protein Databank (Brookhaven National Laboratory)
    1. /usr/sgremote/data/pdb (QUANTA users).
    2. NIH PUBnet/BeechNut/Mac Software/Science/MacImdad4.0 (MacImdad users).
    3. Also see Network-Based Services.
  3. Cambridge Structural Database (Cambridge Crystallographic Data Centre)
    1. Type "quest -j ", where is any alphanumeric string.
    2. Also see Network-Based Services.
  4. CHARMm (Molecular Simulations, Inc.)
    1. QUANTA.
    2. Coil: Type "initcharmm" (once per login session) and then "charmm22".
  5. CHARMM (NIH, Laboratory of Structural Biology, DCRT)
    1. Coil: Type "charmm23".
    2. By arrangement with the Laboratory of Structural Biology, Molecular Graphics and Simulation Section, DCRT: 496-0148.
  6. Chem3D Plus (Cambridge Scientific)
    1. By arrangement with the Scientific Computing Resource Center, DCRT: 402-3489.
  7. ChemDBS-3D (Chemical Design, Inc.)
    1. By arrangement with the Information Technology Branch, Developmental Therapeutics Program, Division of Cancer Treatment, NCI (zaharevitz@dtpvx2.ncifcrf.gov).
  8. ChemDraw (Cambridge Scientific)
    1. By arrangement with the Scientific Computing Resource Center, DCRT: 402-3489.
  9. ChemIntosh II (SoftShell, Inc.)
    1. By arrangement with the Scientific Computing Resource Center, DCRT: 402-3489.
  10. Chem-X (Chemical Design, Inc.)
    1. By arrangement with the Information Technology Branch, Developmental Therapeutics Program, Division of Cancer Treatment, NCI (zaharevitz@dtpvx2.ncifcrf.gov).
  11. Converter (Biosym Technologies)
    1. Insight II (by arrangement with the Scientific Computing Resource Center, DCRT: 402-3489).
  12. CONCORD (Tripos Associates)
    1. SYBYL (by arrangement with the Scientific Computing Resource Center, DCRT: 402-3489).
  13. Discover (Biosym Technologies)
    1. Insight II or stand-alone (by arrangement with the Scientific Computing Resource Center, DCRT: 402-3489).
    2. By arrangement with the Frederick Biomedical Supercomputing Center: 301-846-5532.
  14. Insight II (Biosym Technologies)
    1. By arrangement with the Scientific Computing Resource Center, DCRT: 402-3489.
  15. ISIS Draw (Molecular Design, Ltd.)
    1. By arrangement with the Scientific Computing Resource Center, DCRT: 402-3489.
  16. QUANTA (Molecular Simulations, Inc.)
    1. Via the NIH network - requires a networked Silicon Graphics Workstation. Contact cmb@helix.nih.gov for info.
    2. By arrangement with the Scientific Computing Resource Center, DCRT: 402-3489.
  17. SYBYL (Tripos Associates)
    1. By arrangement with the Scientific Computing Resource Center, DCRT: 402-3489.

Software Suppliers

denotes that a WWW site is maintained by the supplier.
denotes that an FTP site is maintained by the supplier.
denotes that a Gopher site is maintained by the supplier.

  1. Aarhus Univ., Denmark
  2. American Chemical Society Software Div.
  3. BioByte Corp.
  4. Biosym Technologies, Inc.
  5. Brookhaven National Laboratory
  6. CAChe Scientific, Inc.
  7. Cambridge Crystallographic Data Centre
  8. Cambridge Scientific Computing, Inc.
  9. Cambridge University
  10. Chemical Abstracts Service
  11. Chemical Design, Inc.
  12. Columbia University in the City of New York (W. Clark Still)
  13. Columbia University in the City of New York (Anthony Nicholls)
  14. Cray Research
  15. Duke University (David Richardson)
  16. eduSoft, LC
  17. EMBL (Chris Sander, Uwe Hobohm)
  18. Gaussian, Inc.
  19. Harvard Univ. (Martin Karplus)
  20. HyperCube, Inc.
  21. IBM Corporation
  22. Iowa State Unv. (Mark Gordon)
  23. Karolinska Institute (Per Kraulis)
  24. Los Alamos National Laboratory (Gene Carter)
  25. Ludwig Maximilians University, Munich (Helmut Heller)
  26. Minnesota Supercomputer Center, Inc.
  27. Molecular Applications Group
  28. Molecular Design Ltd.
  29. Molecular Simulations, Inc.
  30. NIH, Division of Computer Research and Technology (Bernard Brooks)
  31. NIH, National Cancer Institute, Laboratory of Molecular Biology (B.K. Lee)
  32. NIH, National Cancer Institute, Division of Cancer Therapy (Dan Zaharevitz)
  33. Oxford Molecular, Inc.
  34. PSI International
  35. Quantum Chemistry Program Exchange Gopher
  36. Scripps Research Institute
  37. SemiChem
  38. SoftShell International
  39. Tripos Associates
  40. University College, London
  41. University of Alabama (Mike Carson)
  42. University of Arizona (Pat Walters)
  43. University of Bayreuth (A. Kerber)
  44. University of California at San Francisco (Robert Langridge)
  45. University of California at San Francisco (Irwin Kuntz)
  46. University of California at San Francisco (Peter Kollman)
  47. University of Edinburgh (Roger Sayle)
  48. University of Florida (Michael Zerner)
  49. University of Illiois, Urbana-Champaign (Theoretical Biophysics Group, Beckman Institute for Advanced Science and Technology)
  50. University of Minnesota
  51. University of Ottawa (Stephen Evans)
  52. University of Salzburg (Manfred J. Sippl)
  53. University of Washington (Ethan Merritt)
  54. Wavefunction, Inc.
  55. Yale University (F.M. Richards)

Software With Associated WWW Sites

Note that the following are direct links to other WWW servers.
  1. AMBER (Peter Kollman, UCSF)
  2. Various CSC products, including Chem3D and ChemDraw (Cambridge Scientific Computing, Inc.)
  3. EGO (H. Heller, Ludwig Maximilians Univ., Munich)
  4. HBPLUS (I.K. McDonald, University College, London)
  5. MacroModel (W. Clark Still, Columbia Univ.)
  6. Midas Plus (Tom Ferrin, UCSF)
  7. Various MSI products, including QUANTA, CERIUS2, and Polygraf (Molecular Simulations, Inc.)
  8. MOLGEN+ (University of Bayreuth, Germany)
  9. MolView (Tom Smith, Indiana Univ.-Purdue Univ.)
  10. Namot (Eugene Carter, Los Alamos)
  11. "O" (Morten Kjeldgaard, Aarhus Univ., Denmark)
  12. Various Oxford Molecular products (Oxford Molecular, Inc.)
  13. Parallel CHARMM (Milan Hodoscek, National Institute of Chemistry, Slovenia)
  14. Raster3D (Ethan Merritt, Univ. of Washington via Univ. of Zurich)
  15. UniChem (Cray Research)

Software With Available Electronic Documentation

Note that the following are direct links to other WWW servers.
  1. Various Biosym products, including InsightII and Discover (Biosym Technologies, via Univ. of Zurich)
  2. CHARMm (Molecular Simulations, Inc.)
  3. CHARMM (Milan Hodoscek, National Institute of Chemistry, Slovenia)
  4. HBPLUS (I.K. McDonald, University College, London)
  5. MolScript (Per Kraulis, Uppsala Univ., Sweden via Univ. of Zurich)
  6. Namot (Eugene Carter, Los Alamos)
  7. "O" (Morten Kjeldgaard, Aarhus Univ., Denmark)
  8. RasMol (Roger Sayle, Glaxo Research and Development, UK)
  9. What If (G. Vriend, EMBL)
  10. XMol (Minnesota Supercomputer Center, Inc.)

Multi-Purpose Packages

Multi-purpose packages attempt to be all things to all people. Such software can be viewed as collections of tools that function in a uniform, integrated environment.

  1. CAChe (CAChe Scientific, Inc.)
  2. Chem-X (Chemical Design, Inc.)
  3. Insight II/Discover (Biosym Technologies)
  4. MacroModel (Columbia University)
  5. QUANTA/CHARMm (Molecular Simulations, Inc.)
  6. SYBYL (Tripos Associates)

Personal Computer-Based Packages

Personal computer-based packages tend to offer highly limited functionality, but the convenience of operating in a hardware environment that is familiar to most scientists. Some personal computer based products are dependent on a second component that runs on a Unix computer. This division of labor is called a client-server system.

  1. Alchemy III (Tripos Associates)
  2. CaChe (client) (CaChe Scientific, Inc.)
  3. Chem3D Plus (Cambridge Scientific)
  4. HyperChem (HyperCube, Inc.)
  5. ISIS Base (Molecular Design, Ltd.)
  6. Kinemage (Duke University)
  7. MacImdad (Molecular Applications Group)
  8. MOLGEN+ (University of Bayreuth, Germany)
  9. NanoVision (American Chemical Society)
  10. Nemesis (Oxford Molecular)
  11. RasMol (University of Edinburgh)

Software Listed by Functionality

Chemical Structure Drawing Packages

Chemical structure drawing programs have revolutionized the publication and presentation of chemistry information. In addition, they can be used to input structures to some molecular modeling programs.

  1. ChemDraw (Cambridge Scientific)
  2. ChemIntosh II (SoftShell, Inc.)
  3. ChemWindow (SoftShell, Inc.)
  4. ISIS Draw (Molecular Design, Ltd.)
  5. Kekule (PSI International)

Utilities

  1. Babel (The University of Arizona)

Chemical Structure Databases and Related Software

The databases can be categorized into macromolecular and small organic/organo-metallic collections.

  1. Brookhaven Protein Databank (Brookhaven National Laboratory)
  2. Cambridge Structural Database (Cambridge Crystallographic Data Centre)
  3. CAS-3D (Chemical Abstracts)
  4. The Drug Information System 3D Database (NIH/NCI/DCT)

The following software is used to search the major chemical structure databases:

  1. Quest/Gstat (Search/Access Cambridge Structural Database) (Cambridge Structural Database Centre)
  2. Gopher (Search/Access PDB) (University of Minnesota)
  3. Iditis (Extract structural data from the PDB) (Oxford Molecular)
  4. PROTEP (Search PDB based on structural motifs) (Tripos Associates)

The following software is used to create, maintain, and search local chemical structure databases:

  1. ChemDBS-3D (Chemical Design, Inc.)
  2. 3DB UNITY (Tripos Associates)
  3. ISIS Host (Molecular Design, Ltd.)

Model Building

  1. Converter (Biosym Technologies)
  2. Cobra (Oxford Molecular)
  3. CONCORD (Tripos Associates)
  4. CONCORD (Tripos Associates)
  5. MOLGEN+ (University of Bayreuth, Germany)

Computation Engines

Molecular Mechanics

  1. AMBER (public version dist. by UCSF)
  2. CHARMm (Molecular Simulations, Inc.)
  3. CHARMM (NIH LSB)
  4. CHARMM (Harvard Univ.)
  5. Discover (Biosym Technologies)
  6. Polaris (Molecular Simulations, Inc.)

Quantum Chemistry

ab initio:

  1. GAMESS (public version, dist. by QCPE)
  2. GAMESS (Parallel version) (Iowa State Univ.)
  3. HONDO (IBM Corporation)
  4. Gaussian (Gaussian, Inc.)
  5. Spartan (Wavefunction, Inc.)
  6. UniChem (Cray Research)

Semiempirical:

  1. AMPAC (SemiChem, Inc.)
  2. AMPAC (public version, dist. by QCPE)
  3. MOPAC (public version dist. by QCPE)
  4. MOPAC (public version dist. by QCPE)
  5. MOPAC (Fujitsu, dist. by QCPE)
  6. Vamp (Oxford Molecular)
  7. ZINDO (University of Florida)
Density Functional Theory:

  1. DMol (Biosym Technologies)

Geometry Engines

Distance Geometry

  1. DGEOM (Dupont, dist. by QCPE)
  2. DGII (QCPE)
  3. Distance Geometry Feature of SYBYL (Tripos Associates)
  4. Distance Geometry Feature of XPLOR (Molecular Simulations, Inc.)

NMR-Based Structure Determination

  1. CHARMM
  2. DGEOM
  3. DSPACE (Biosym Technologies)
  4. HyperNMR (HyperCube, Inc.)
  5. NMRchitect (Biosym Technologies)
  6. NMR Structure (Molecular Simulations, Inc.)
  7. XPLOR (Molecular Simulations, Inc.)

Molecular Dynamics

  1. AMBER (public version dist. by UCSF)
  2. CHARMM
  3. CHARMm (Molecular Simulations, Inc.)
  4. CHARMM (NIH LSB)
  5. CHARMM (Harvard Univ.)
  6. Discover (Biosym Technologies)
  7. EGO (Ludwig Maximilians Univ., Munich)
  8. XPLOR (Molecular Simulations, Inc.)

Conformational Searching

  1. CAChe (CAChe Scientific, Inc.)
  2. Chem-X (Chemical Design, Inc.)
  3. Cobra (Oxford Molecular)
  4. Insight II/Discover (Biosym Technologies)
  5. MacroModel (Columbia University)
  6. QUANTA/CHARMm (Molecular Simulations, Inc.)
  7. SYBYL (Tripos Associates)

Graphics Engines

 See also Personal Computer-Based Packages.
  1. GEMM (NIH)
  2. GRASP (Columbia University)
  3. Light/Light-Movie (NIH)
  4. Midas Plus (UCSF)
  5. MolScript (Karolinska Institute)
  6. "O" (Aarhus University, Denmark)
  7. RasMol (University of Edinburgh)
  8. Raster3D (University of Washington)
  9. Ribbons (University of Alabama)
  10. Setor (University of Ottawa)
  11. Visual Molecular Dynamics (VMD) (University of Illinois, Urbana-Champaign)
  12. XMol (Minnesota Supercomputer Center, Inc.
  13. XtalView (Scripps Institute)

Software Listed by Application Area

Biopolymers

Proteins

  1. AbM (Antibody Modeling) (Oxford Molecular)
  2. Cameleon (Oxford Molecular)
  3. Composer (Tripos Associates)
  4. DEFINE_Structure (Yale University)
  5. DSSP and related databases (EMBL)
  6. HBPlus (University College, London)
  7. Homology (Biosym Technologies)
  8. MatchMaker (Tripos Associates)
  9. PROSA II (University of Salzburg)
  10. Protein Design (Molecular Simulations, Inc.)
  11. What If (Gert Vriend, EMBL)

Nucleic Acids

  1. NAMOT (Los Alamos National Laboratory)

Structure-Activity

  1. Anaconda (Oxford Molecular)
  2. Apex (Biosym Technologies)
  3. Asp (Oxford Molecular)
  4. CoMFA (Tripos Associates)
  5. DISCO (Tripos Associates)
  6. Pomona College Models (BioByte)
  7. RECEPTOR (Tripos Associates)
  8. RECEPTOR (Molecular Simulations, Inc.)
  9. SYBYL QSAR Module (Tripos Associates)
  10. Tsar (Oxford Molecular)

Docking/Structure-Based Molecular Design

  1. Dock (UCSF)
  2. LEAPFROG (Tripos Associates)
  3. Ludi (Biosym Technologies)