Protein Structure Resources
Software  Lists of Resources  Organizations Summer
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.
UHBD 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.

APBS

 

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. 
Chemical Computing Group
  YASARA
  Amsterdam Density Functional (ADF) package
List at PDB A list of software at the Protein Data Bank.
List at C2B2 A List at the Center for Computational Biology and Bioinformatics.
  DINO
  SoftBerry
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 - The FFAS03 server provides an interface to the third generation of the profile-profile alignment and fold recognition algorithm FFAS.
  Proteome Analyst
  PCE - Protein Continium electrostatics
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
Summer

LANL - Appointments can be three months or less, an academic semester, or a full academic year or sabbatical. The opportunities are limited by available collaborations and/or funding sources.

PNNL- FaST

PNNL-Summer

   
Research Groups
David Baker
Michael Levitt

Vijay Pande

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

Teresa Head-Gordon
  Roberto Car
Donald Bashford
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

   
   
   
   
Organizations

 SMB  Society for Mathematical Biology
 ISCB - International Society for Computational Biology
EBI - European Bioinformatics Institute
   
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
 NIH
   Dicty Workbench
 
Databases

MetaDB: A Metadatabase for the Biological Sciences

PDB