- Netlib: a collection of mathematical software, papers, and databases.
- PETSc: a software library for parallel solution of partial differential equations with the MPI standard for all message-passing communication.
- MPI: Message-Passing Interface Standard
- MPI Home Page by Argonne National Laboratory.
- LAM (Local Area Multicomputer): an MPI programming environment and development system for heterogeneous computers on a network.
- MGNet: A repository for information related to multigrid, multilevel, multiscale, aggregation, defect correction, and domain decomposition methods.
- The Finite Element Circus
- TOP500 Supercomputer Sites

- CHARMM: 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. See CHARMM c29b2 Documentation and CHARMM .doc HOME in NIH/NHLBI/LBC for the details.
- A short introduction to molecular synamics simulations
- DelPhi: A widely used software package for computing electrostatic potentials for molecules of arbitrary shape and charge distribution. It can solve the non-linear and linear Poisson-Boltzman equation by finite difference solvers on a cubical lattice.
- 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.
- NAMD : A parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems by Theoretical and Computational Biophysics Group at the University of Illinois at Urbana-Champaign. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using switched fast ethernet.
- VMD (Visual Molecular Dynamics): A molecular visualization program for displaying, animating, and analyzing biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc.
- 2001 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
- Amos' WWW links page: 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.

- AMS: American Mathematical Society
- SIAM
- MAA
- Mathematical Programming Society
- SIAM Activity Group on Optimization
- Society for Mathematical Biology

- MathSciNet
- Front for the Mathematics ArXiv
- MGNet: a repository for information related to multigrid, multilevel, multiscale, aggregation, defect correction, and domain decomposition methods.
- Mathematics web sites around the world
- Mathematics WWW Virtual Library
- Computational Mathematics Archive
- Internet Mathematics Library