program packages, software libraries, etc.

theoretical chemistry

(see also: molecular modelling)

global optimization, docking, folding, …

molecular viewers/manipulators

  • RasMol
  • enhanced RasMol, by UC Berkeley
  • Molden (here is a brief description of the two main control windows)
  • Jmol, an OpenScience/open source molecule viewer and editor
  • Marvin, a Java program for drawing/displaying chemical structures on the web
  • gOpenMol by Leif Laaksonen, part of the OpenMol project by Geerd Diercksen (Garching) (gOpenMol now also comes with a tutorial)
  • Spock, a molecular graphics program by Jon A. Christopher (runs also under Linux!)
  • VMD, visual molecular dynamics, by Klaus Schulten’s Theoretical Biophysics Group at the University of Illinois (also responsible for the NAMD molecular dynamics code)
  • Molekel by Stefan Portmann, Swiss Center for Scientific Computing
  • Structural biology software database by the Klaus Schulten group
  • PyMOL (see also this link)
  • Chemtool, a molecular graphics program for linux (see also this older link)
  • WhatIf, a protein structure viewer, analysis, and manipulation program with many useful features (see also this link for a web interface to some features)
  • XCrysDen, a solid state and molecules visualization program, with interfaces to Gaussian, Crystal, PWscf, Wien2k,…
  • XMakeMol by Matt Hodges
  • Ghemical, semiempirical CompChem package with a molecule builder
  • Ghemical-GMS, a special Ghemical version as front- and back-end for Gamess
  • Gabedit (reads molecule data and molpro/Gaussian output; can produce povray input files)
  • Mol2Mol, visual conversion between various molecule file formats, with PoVRay output (sorry, only windows)
  • Dino3D, visualization of biomolecules, surfaces, etc. (these pages also include a nice intro to povray)
  • UCSF Chimera molecular viewer
  • PoVRay raytracer

general scientific computing

(see also: mathematics)

typesetting and text processing

  • DANTE, Deutschsprachige Anwendervereinigung TeX, with link to the comprehensive TeX Archive Network CTAN and other helpful links…
  • TeX Users Group, with links to all of the above, plus a lot of other useful stuff, including acollection of TeX-related mailing lists
  • TeX2gif, conversion of LaTeX to gif (e.g. for displaying LaTeX equations in MS-Word or on web pages)

Last updated on Wed Jan 09 08:45:54 MET DST 2013