See also:

• Science: Biology: Biochemistry and Molecular Biology: Biomolecules: Proteins and Enzymes: Structure  (37)
• Science: Biology: Biochemistry and Molecular Biology: Software  (17)
• Science: Biology: Bioinformatics: Online Services  (174)
• Science: Chemistry: Software  (233)
• Science: Physics: Crystallography: Software  (61)

Amber  amber.ch.ic.ac.uk A general purpose molecular mechanics and molecular dynamics package with the capability to compute free-energy changes.

AMMP  www.cs.gsu.edu/~cscrwh/ammp/ammp.html A free program suite for molecular mechanics, dynamics and modeling with some special features like docking or ab initio DFT calculations. Runs under Linux/Unix and Win9x. The site provides access to the documentation and offers on-line tutorials.

Ascalaph DNA  www.agilemolecule.com/Ascalaph/Ascalaph_DNA.html Program for creating models of nucleic acids and their complexes with low-molecular-weight and protein ligands.

AutoDock  www.scripps.edu/pub/olson-web/doc/autodock A suite of automated docking tools. It is designed to predict how small flexible molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.

B: On-line Molecular Modeling  www.scripps.edu/case/Biomer "B" (formerly known as Biomer) is a Java-based molecular modeling program for small organic molecules and biopolymers. Supports nucleic acids (DNA/RNA), polypeptides, polysaccharides, the AMBER force field, geometry optimization, simulated annealing. Exports jpeg, gif, and ppm images.

BioAdviser  www.fqs.pl/life_science/bioadviser Package for displaying, analyzing, and manipulating 3D structures of biological macromolecules, with special emphasis on the study of proteins and enzymes. Includes links to other products by FQS Poland, in Krakow.

Bioinformatics Tools  darwin.nmsu.edu/molb_resources/bioinformatics Sequence analysis tools including protein classification with the assistance of predicted secondary structure and sequence format tools, available from the Molecular Biology Program at New Mexico State University.

CHARMM  brooks.chem.lsa.umich.edu/charmm_docs/TSRI_docs-list.htm A program for macromolecular dynamics and mechanics. It performs standard molecular dynamics in many different ensembles (e.g., NVE, NVT, NPT) using state-of-the-art algorithms for timestepping, long range force calculation and periodic images.

ChemVis  www2.chemie.uni-erlangen.de/projects/ChemVis Visualization of physico-chemical structures in VML, from research at the Universities of Stuttgart and Erlangen in Nürnberg, Germany.

EGO  www.lrz-muenchen.de/~heller/ego A parallel program for molecular dynamics simulations of biomolecules.

EGO VIII  www.lrz-muenchen.de/~heller/ego/egointro.html A program to perform molecular dynamics simulations on parallel as well as on sequential computers.

Folding@home  folding.stanford.edu It is a distributed computing project which studies protein folding, misfolding, aggregation, and related diseases.

Genoscience  www.3dgenoscience.com Genmol is a 3D molecular modeling software for measuring resistance/affinity between a ligand and a target, used for disease management and drug discovery. Details of company in Marseille, France.

Ghemical  www.uku.fi/~thassine/projects/ghemical An easy-to-use molecular editor and modeling package with all-atoms molecular mechanics, reduced protein models and links to many common chemistry programs. Ghemical is released under the GNU GPL and includes source code.

GrAfSS: Graph Theoretic Applications for Structure Searching  grafss.imfr.net Graph theoretic methods for the analysis of structural relationships in biological macromolecules.

Gromacs  www.gromacs.org A molecular dynamics package primarily designed for biomolecular systems such as proteins and lipids. It is a free software.

GROMOS  www.igc.ethz.ch/GROMOS A general-purpose molecular dynamics computer simulation package for the study of biomolecular systems.

Highlights of Biochemistry  www.biologie.uni-hamburg.de/lehre/bza/eanfang.htm Molecular structures are made visible, dependent on Chime scripts at the Faculty of Biology, University of Hamburg, Germany.

IMB Jena Image Library of Biological Macromolecules  www.imb-jena.de/IMAGE.html Resource for visualization and analysis of 3D-biopolymer structures; proteins, nucleic acids, carbohydrates, and small molecule ligands. Combines experimental and computer generated models, maintained in Germany.

Jay Ponder Lab  dasher.wustl.edu Graphical user interface to suites of molecular modeling tools, providing an integrated environment for engineering applications. Contacts for the group at Washington University School of Medicine in Saint Louis, Missouri.

NAMD  www.ks.uiuc.edu/Research/namd A parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code.

Pande Group  www.stanford.edu/group/pandegroup Folding simulations for fusion peptides, proteins and RNA with aim of predicting structure from genome by research at Stanford University, California.

PDB Viewer  www.geocities.com/pdbviewer Downloads for Windows and Linux, to visualize three dimensional structure of macromolecules, using protein data bank format for atom coordinates, from ex-student at University of Manchester, England.

Prion Helical Wheels  www.mad-cow.org/~tom/helical_wheel.html Java applet to illustrate alpha-helices, using a traditional helical wheel. Output as Postscript, JPEG, GIF or PICT.

Protein Structure Database  www.psc.edu/~deerfiel/PSdb PSdb uses primary data, to relate secondary and tertiary information, for solvent accessibility, internal relative distances, and ligand interactions. Maintained at the Mellon Institute, Pittsburgh, Pennsylvania.

RAMP  software.compbio.washington.edu/ramp/ramp.html Public domain suite of programs to aid in the modeling of protein three-dimensional structures. Tested on Linux and Unix.

Sesame Project  www.sesame.wisc.edu Protein structure-function software in multiple modules, maintained at the University of Wisconsin, Madison.

SWISS-MODEL  swissmodel.expasy.org//SWISS-MODEL.html SWISS-MODEL is an Automated Protein Modelling Server running at the GlaxoWellcome Experimental Research in Geneva, Switzerland.

TINKER  dasher.wustl.edu/tinker A free molecular modeling package for molecular mechanics and dynamics, with some special features for biopolymers. Distributed as source code and as binaries for Windows9x, Linux and Mac.

WhatIf  www.cmbi.ru.nl/whatif Protein structure analysis software for Linux, SGI/IRIX, Windows NT. Performs mutant prediction, structure verification, homology modeling and molecular visualization. Links to the documentation in HTML. Commercial software.

X-plor Archives  www.bio.net/hypermail/X-PLOR Forum for 3D macromolecular structure determination. Includes links to other Biosci/Bionet newsgroups, maintained at Indiana University, Bloomington.

YASARA  www.yasara.org (Yet Another Scientific Artificial Reality Application) is an interactive real-time molecular dynamics program.

ZMM Software Inc.  www.zmmsoft.com Modeling tool for theoretical studies, employing molecular mechanics approach in combination with Monte Carlo energy minimization algorithm. Downloads on secure server, and contacts in Flamborough, Ontario.