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Biochemistry Software

AMBER
Assisted Model Building with Energy Refinement. Allows macromolecular simulations.

Biology WorkBench
Access to protein and nucleic acid databases, and selection of software for crystallographers. From the San Diego Supercomputer Center, University of California at San Diego.

Biomolecular Modeling Laboratory
Software and databases allowing manipulations of protein/nucleic acid structures. From Imperial Cancer Research Fund.

Biomolecular Structure and Modelling
Software collection provided by University College London.

BioToolKit
Search for biotechnology hardware and software suppliers.

Blocks WWW Server
Use their collection of programs to search for protein sequence homology. From Fred Hutchinson Cancer Research Center.

Chemistry Software.com
Wide selection of analytical, educational, and lab management software.

Combinatorial Extension of the Optimal Path
Aligning polypeptide sequences. From Ilya N. Shindyalov and Philip E. Bourne.

Computational Molecular Biology at NIH
Nucleic acid and protein sequence analysis tools and software. From the US National Institutes of Health.

Computational Biology Tools
Software packages align, fold, and analyze protein and peptide sequences. From Cornell University.

Frieden, Carl
KINSIM/FITSIM, enzyme kinetics simulation package. Washington University School of Medicine.

Gepasi
Simulates fluxes through metabolic pathways. From University of Wales at Aberystwyth.

MODELLER
Compares homologies of 3-D protein structures.

Molecular Biology Notebook
CD-ROM simulation of molecular biology experiments. From Nathalie Castells-Brooke, Institute of Arable Crops Research, Rothamsted, UK.

Molecular Simulations
Distributors of molecular modeling and molecular biology software.

Naccess
Uses a Protein Data Bank file to determine solvent accessible areas.

PROMISE
Prosthetic groups and metal ions in protein active sites database. From the University of Leeds.

Protein Sidechain Webpage
Sidechain rotamer libraries, conformation prediction, and analysis.

Richardson's 3-D Protein Structure Homepage
Learn how to rotate protein images generated by MAGE and PREKIN programs. From David C. and Jane S. Richardson, Duke University.

Spin Up
Software and hardware offerings are applicable to graphics, molecular biology, molecular modeling, and spectroscopy.

Structural Classification of Proteins
Determines structural and evolutionary similarities of different proteins.

Visual Molecular Dynamics
3-D graphics program for visualization of nucleic acid, protein, and lipid systems. From the University of Illinois at Urbana-Champaign.

WHAT IF
Protein modeling and visualization program.