a collection of mathematical software, papers, and databases.
- FEniCS Project :
a collection of free software with an extensive list of features for automated, efficient solution of differential equations.
a software library for parallel solution of partial differential equations
with the MPI standard for all message-passing communication.
Message-Passing Interface Standard
- 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
Midwest Numerical Analysis Day
- TOP500 Supercomputer Sites
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
- CHARMM tutorial
- DelPhi: Provides numerical solutions to the Poisson-Boltzmann equation (both linear and nonlinear form) for molecules of arbitrary shape and charge distribution.
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
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.