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Top: Science: Biology: Biochemistry_and_Molecular_Biology: Biomolecules: Software:

Software (35)

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Sites:

http://www.cs.gsu.edu/~cscrwh/ammp/ammp.html   » AMMP Open in a new browser window
   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.
   http://www.cs.gsu.edu/~cscrwh/ammp/ammp.html

http://amber.ch.ic.ac.uk/   » Amber Open in a new browser window
   A general purpose molecular mechanics and molecular dynamics package with the capability to compute free-energy changes.
   http://amber.ch.ic.ac.uk/

http://www.scripps.edu/pub/olson-web/doc/autodock/   » AutoDock Open in a new browser window
   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.
   http://www.scripps.edu/pub/olson-web/doc/autodock/

http://www.scripps.edu/case/Biomer/   » B: On-line Molecular Modeling Open in a new browser window
   "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 ann
   http://www.scripps.edu/case/Biomer/

http://www.fqspl.com.pl/bioadviser/   » BioAdviser Open in a new browser window
   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.
   http://www.fqspl.com.pl/bioadviser/

http://home.pchome.com.tw/team/gentamicin/mol/mol.htm   » CADD tools in Drug R&D Open in a new browser window
   PSCAN, PMOL2Q, DBFILTER download page. Taichung, Taiwan.
   http://home.pchome.com.tw/team/gentamicin/mol/mol.htm

http://www.scripps.edu/brooks/charmm_docs/charmm.html   » CHARMM Open in a new browser window
   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.
   http://www.scripps.edu/brooks/charmm_docs/charmm.html

http://www2.chemie.uni-erlangen.de/projects/ChemVis/   » ChemVis Open in a new browser window
   Visualization of physico-chemical structures in VML, from research at the Universities of Stuttgart and Erlangen in Nürnberg, Germany.
   http://www2.chemie.uni-erlangen.de/projects/ChemVis/

http://www.cse.clrc.ac.uk/msi/software/DL_POLY/   » DL Poly Open in a new browser window
   A parallel molecular dynamics simulation package.
   http://www.cse.clrc.ac.uk/msi/software/DL_POLY/

http://www.lrz-muenchen.de/~heller/ego/   » EGO Open in a new browser window
   A parallel program for molecular dynamics simulations of biomolecules.
   http://www.lrz-muenchen.de/~heller/ego/

http://www.lrz-muenchen.de/~heller/ego/egointro.html   » EGO VIII Open in a new browser window
   A program to perform molecular dynamics simulations on parallel as well as on sequential computers.
   http://www.lrz-muenchen.de/~heller/ego/egointro.html

http://folding.stanford.edu/   » Folding@home Open in a new browser window
   It is a distributed computing project which studies protein folding, misfolding, aggregation, and related diseases.
   http://folding.stanford.edu/

http://igc.ethz.ch/gromos/   » GROMOS Open in a new browser window
   A general-purpose molecular dynamics computer simulation package for the study of biomolecular systems.
   http://igc.ethz.ch/gromos/

http://www.3dgenoscience.com/   » Genoscience Open in a new browser window
   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.
   http://www.3dgenoscience.com/

http://www.uku.fi/~thassine/projects/ghemical/   » Ghemical Open in a new browser window
   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.
   http://www.uku.fi/~thassine/projects/ghemical/

http://kael.net/helical.htm   » Helical Wheels Open in a new browser window
   Java applet to illustrate alpha-helices, using a traditional helical wheel. Output as Postscript, JPEG, GIF or PICT.
   http://kael.net/helical.htm

http://www.biologie.uni-hamburg.de/lehre/bza/eanfang.htm   » Highlights of Biochemistry Open in a new browser window
   Molecular structures are made visible, dependent on Chime scripts at the Faculty of Biology, University of Hamburg, Germany.
   http://www.biologie.uni-hamburg.de/lehre/bza/eanfang.htm

http://www.imb-jena.de/IMAGE.html   » IMB Jena Image Library of Biological Macromolecules Open in a new browser window
   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.
   http://www.imb-jena.de/IMAGE.html

http://dasher.wustl.edu/   » Jay Ponder Lab Open in a new browser window
   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.
   http://dasher.wustl.edu/

http://jrgm.ourprofile.org/   » Molecular Modeling on Your Home Computer Open in a new browser window
   Introduction to a quick, simple, and free way to model molecules.
   http://jrgm.ourprofile.org/

http://www.ks.uiuc.edu/Research/namd/   » NAMD Open in a new browser window
   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.
   http://www.ks.uiuc.edu/Research/namd/

http://www.geocities.com/pdbviewer/   » PDB Viewer Open in a new browser window
   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.
   http://www.geocities.com/pdbviewer/

http://www.stanford.edu/group/pandegroup/   » Pande Group Open in a new browser window
   Folding simulations for fusion peptides, proteins and RNA with aim of predicting structure from genome by research at Stanford University, California.
   http://www.stanford.edu/group/pandegroup/

http://proteindynamics.com/   » Protein Dynamics, Inc. Open in a new browser window
   Molecular dynamics simulation programs for proteins, DNA, and RNA, including 3D viewing of molecules. Offers downloadable demonstration version, from Milpitas California.
   http://proteindynamics.com/

http://www.psc.edu/~deerfiel/PSdb/   » Protein Structure Database Open in a new browser window
   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.
   http://www.psc.edu/~deerfiel/PSdb/

http://zebra.berkeley.edu/raft/   » RAFT Open in a new browser window
   Rapid Autonomous Fragment Test: interface to search library of known protein folds for automously folding units and subdomains.
   http://zebra.berkeley.edu/raft/

http://software.compbio.washington.edu/ramp/ramp.html   » RAMP Open in a new browser window
   Public domain suite of programs to aid in the modeling of protein three-dimensional structures. Tested on Linux and Unix.
   http://software.compbio.washington.edu/ramp/ramp.html

http://swissmodel.expasy.org//SWISS-MODEL.html   » SWISS-MODEL Open in a new browser window
   SWISS-MODEL is an Automated Protein Modelling Server running at the GlaxoWellcome Experimental Research in Geneva, Switzerland.
   http://swissmodel.expasy.org//SWISS-MODEL.html

http://www.sesame.wisc.edu/   » Sesame Project Open in a new browser window
   Protein structure-function software in multiple modules, maintained at the University of Wisconsin, Madison.
   http://www.sesame.wisc.edu/

http://www.swbic.org/products/bioinfo/bioinfo.php   » Southwest Biotechnology and Informatics Center Open in a new browser window
   Sequence analysis tools including protein classification with the assistance of predicted secondary structure and sequence format tools, available under license from New Mexico State University.
   http://www.swbic.org/products/bioinfo/bioinfo.php

http://dasher.wustl.edu/tinker/   » TINKER Open in a new browser window
   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.
   http://dasher.wustl.edu/tinker/

http://www.cmbi.ru.nl/whatif/   » WhatIf Open in a new browser window
   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.
   http://www.cmbi.ru.nl/whatif/

http://www.bio.net/hypermail/X-PLOR/   » X-plor Archives Open in a new browser window
   Forum for 3D macromolecular structure determination. Includes links to other Biosci/Bionet newsgroups, maintained at Indiana University, Bloomington.
   http://www.bio.net/hypermail/X-PLOR/

http://www.yasara.org/   » YASARA Open in a new browser window
   (Yet Another Scientific Artificial Reality Application) is an interactive real-time molecular dynamics program.
   http://www.yasara.org/

http://www.zmmsoft.com/   » ZMM Software Inc. Open in a new browser window
   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.
   http://www.zmmsoft.com/


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Last Updated: 2006-08-03 12:20:14


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