Protein Structure Resources
Software  Lists of Resources  Organizations  
Servers  Distributed Computing    
Centers  Conferences    
Research Groups  Journals    
Software

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
VMD (Visual Molecular Dynamics) is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
GROMACS (GROMACS Runs On Most All Computer Systems) is a package to perform molecular dynamics. It is primarily designed for biochemical molecules like proteins and lipids.
NWChem
AMBER
CPMD - The CPMD code is a parallelized plane wave/pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics.
Clustermatic is a collection of technologies for a new cluster architecture. The new architecture runs an operating system that provides a single system image of the entire cluster.
The UHBD (University of Houston Brownian Dynamics) program is capable of solving the linearized and non-linear Poisson-Boltzmann equation. The program has the capability to compute electrostatic free energies of binding of two molecules.
Chemical Computing Group
YASARA
Amsterdam Density Functional (ADF) package
A list of software at the Protein Data Bank.
A list of softwareat the Center for Computational Biology and Bioinformatics.
DINO
SoftBerry
  accelrys
  ProteinShop
   
Servers
Robetta is a full-chain protein structure prediction server.
Rosetta Design
Superfamily is a Hidden Markov Model library and genome assignments server.
The aim of the ProFunc server is to help identify the likely biochemical function of a protein from its three-dimensional structure.
BLAST - The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
FFAS03
FFAS03 - The FFAS03 server provides an interface to the third generation of the profile-profile alignment and fold recognition algorithm FFAS.

Proteome Analyst

Proteome Analyst
PCE - Protein Continium electrostatics
APBS (Adaptive Poisson-Boltzmann Solver) is a software package for the numerical solution of the Poisson-Boltzmann equation, one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. 
  SCALI - Structural Core ALIgnment of proteins
   
Centers
The Protein Structure Initiative (PSI) is a federal, university, and industry effort to reduce the costs and lessen the time it takes to determine a three-dimensional protein structure. The long-range goal of the PSI is to make the three-dimensional atomic-level structures of most proteins easily obtainable from knowledge of their corresponding DNA sequences. PSI Centers
Bioscience Division integrates biology, chemistry, physics, and computational sciences to build a strong scientific and technological base for addressing the complex problems that face the nation.

The W.M. Keck Center for Computational and Structural Biology Mission: To provide a world-class environment for interdisciplinary research training at the interface between biological and biomedical sciences and the computational, physical, mathematical and engineering sciences.

 

UCLA-DOE Laboratory of Structural Biology and Molecular Medicine (LSBMM), the Laboratory has as its revised mission: (1) The partnering of structural and computation biology in the determination of folds for proteins in genomes, and the analysis of function and interactions from genome sequences. (2) The development of molecular nuclear medicine, including new diagnostic biological imaging procedures and their relationship to drug therapies to improve the quality of life.
PNNL-MSCF Pacific Northwest National Lab - Molecular Science Computing Facility
SNL - Computational Biology at Sandia National Labs
SIB - Swiss Institute of Bioinformatics
C2B2 - Center for Computational Biology and Bioinformatics at Columbia University.
The Scripps Research Institute
  National Center for Research Resources: Biomedical Technology Research Resources Directory
  Beckman Institute
  PNNL-EMSL
  PNNL-EMSL-Molecular Science Computing Facility
Quantum Protein Centre
   
   
 
Research Groups
David Baker

Michael Levitt

Vijay Pande

Judith Frydman

Charles Brooks

Donald Bashford

Patricia L. Clark
 Jane Clarke
Cecilia Clementi
Fred E. Cohen
Trevor Creamor
Valerie Dagget
David Eisenberg
 
Martin Gruebele

Teresa Head-Gordon
  Roberto Car
Chris Bystroff
  Dmitri Klimov
   
   
Distributed Computing Projects

Folding@Home

Predictor@Home
Human Proteome Folding Project
 
Journals
Biophysical Journal

Science

Nature
 Nature Biotechnology
Nature Reviews
 Biochemistry
ProteinSpotlight is a monthly review written by the Swiss-Prot team of the Swiss Institute of Bioinformatics.
 
 Protein Science
Cell

NAS Proceedings of the National Academy of Sciences

  Proteins: Structure, Function, and Bioinformatics
   Physics of Life
   Scientific American
   European Biophysics Journal
Organizations

   Society for Mathematical Biology
 ISCB - International Society for Computational Biology
EBI - European Bioinformatics Institute
  European Physical Society - Division of Physics in Life Sciences
  The Protein Society
   
   
   
Projects

Biowulf

Blue Gene
 CAFASP
   FORCASP
Documents

Genetic Algorithms and Protein Folding

Molecular Biophysics Syllabus
  Protein Design
  Prediction of Function from Protein Structure
  A Guide to Structure Prediction
Lists of Resources

LANL Bioinformatics

 
   
   
Conferences

AFP-SIG '05

 
 
   
 

dictyBASE

 Genome
 Dictyostelium discoideum at NIH
   Dicty Workbench
 
Databases

MetaDB: A Metadatabase for the Biological Sciences

PDB
 Structure Function Linkage Database