Xie De Xuan
a collection of mathematical software, papers, and databases.
a software library for parallel solution of partial differential equations
with the MPI standard for all message-passing communication.
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
- TOP500 Supercomputer Sites
Computational Molecular Biology
- 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
- 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.
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.