Scientific Computing


Computational Molecular Biology

  • CHARMM (Chemistry at HARvard Macromolecular Mechanics): A widely-used program package for large scale biomolecular potential energy minimization, molecular dynamics, normal modes and crystal optimizations. It can be used to simulations of proteins, nucleic acids and lipids.
  • A short introduction to molecular synamics simulations
  • CHARMM tutorial
  • DelPhi: Provides numerical solutions to the Poisson-Boltzmann equation (both linear and nonlinear form) for molecules of arbitrary shape and charge distribution.
  • PDB: Protein Data Bank, the single worldwide repository for the processing and distribution of 3-D biological macromolecular structure data (about 20,000 structures of proteins and nucleic acids.
  • VMD (Visual Molecular Dynamics): A molecular visualization program for displaying, animating, and analyzing biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc.
  • 2003 Primer : Genomics and Its Impact on Medicine and Society
  • Dictionary of Genetic Terms
  • PubMed: a service of the National Library of Medicine, provides access to over 12 million MEDLINE citations back to the mid-1960’s and additional life science journals.
  • Annual Conference on Research in Computational Molecular Biology
  • ExPASy: SIB Bioinformatics Resource Portal.
  • Life Science Directory: This list contains almost exclusively pointers to information sources for life scientists with an interest in biological macromolecules.
  • Amino acid structure and properties: from U. Berlin. Includes 3-D interactive models.

Mathematical Organizations

Mathematics Archives