| Protein
Structure Resources |
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| Software |
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NAMD
is a parallel molecular dynamics code designed for high-performance
simulation of large biomolecular systems. |
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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. |
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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. |
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NWChem |
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AMBER |
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CPMD
- The CPMD code is a parallelized plane wave/pseudopotential implementation
of Density Functional Theory, particularly designed for ab-initio
molecular dynamics. |
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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
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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.
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Chemical Computing Group |
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YASARA |
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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. |
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DINO |
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SoftBerry |
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| Servers |
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Robetta
is a full-chain protein structure prediction server. |
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Rosetta
Design |
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Superfamily
is a Hidden Markov Model library and genome assignments server. |
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The aim of the ProFunc
server is to help identify the likely biochemical function of a
protein from its three-dimensional structure. |
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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. |
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FFAS03
- The FFAS03 server provides an interface to the third generation
of the profile-profile alignment and fold recognition algorithm
FFAS. |
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Proteome Analyst
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PCE
- Protein Continium electrostatics |
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| Centers |
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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 |
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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. |
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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.
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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 |
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SNL
- Computational Biology at Sandia National Labs |
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SIB
- Swiss Institute of Bioinformatics |
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C2B2
- Center for Computational Biology and Bioinformatics
at Columbia University. |
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The Scripps Research
Institute |
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| Summer |
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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. |
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PNNL-
FaST
PNNL-Summer
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| Organizations |
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| SMB |
Society
for Mathematical Biology |
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ISCB
- International Society for Computational Biology |
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EBI
- European Bioinformatics Institute |
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| Databases |
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MetaDB:
A Metadatabase for the Biological Sciences |
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PDB |
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