| Directory > Science > Biology > Biochemistry and Molecular Biology > Biomolecules > Software ChemVis
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/
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Highlights of Biochemistry
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
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Pande Group
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/
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GRAMM (Global Range Molecular Matching)
A program for modeling protein docking.
http://reco3.musc.edu/gramm/
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SWISS-MODEL
SWISS-MODEL is an Automated Protein Modelling Server running at the GlaxoWellcome Experimental
Research in Geneva, Switzerland.
http://www.expasy.ch/swissmod/SWISS-MODEL.html
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EGO
A parallel program for molecular dynamics simulations of biomolecules.
http://www.lrz-muenchen.de/~heller/ego/
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DL Poly
A parallel molecular dynamics simulation package.
http://www.cse.clrc.ac.uk/msi/software/DL_POLY/
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YASARA
(Yet Another Scientific Artificial Reality Application) is an interactive real-time molecular
dynamics program.
http://www.yasara.org/
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Amber
A general purpose molecular mechanics and molecular dynamics package with the capability to compute
free-energy changes.
http://amber.ch.ic.ac.uk/
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Genmol
Genmol is a 3D molecular modeling software for measuring resistance/affinity between a ligand and a
target, used for Disease Management, Drug Discovery and Development of molecules.
http://www.3dgenoscience.com/index.php
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Biomolecular Modeling Information Server
Web resources including: theory and methods of computational modeling, alphabetical software and
database directory.
http://www.mol.uj.edu.pl/modmol/frontpage.htm
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Folding@home
It is a distributed computing project which studies protein folding, misfolding, aggregation, and
related diseases.
http://folding.stanford.edu/
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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.
http://dasher.wustl.edu/tinker/
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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.
http://www.uku.fi/~thassine/ghemical/
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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.
http://www.scripps.edu/pub/olson-web/doc/autodock/
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B: On-line Molecular Modeling
"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.
http://www.scripps.edu/case/Biomer/
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CHARMM
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
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Helical Wheels
Java applet to illustrate alpha-helices, using a traditional helical wheel. Output as Postscript,
JPEG, GIF or PICT.
http://marqusee9.berkeley.edu/kael/helical.htm
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EGO VIII
A program to perform molecular dynamics simulations on parallel as well as on sequential computers.
http://www.lrz-muenchen.de/~heller/ego/egointro.html
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AMMP
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
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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.
http://www.cmbi.kun.nl/whatif/
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RAFT
Rapid Autonomous Fragment Test: interface to search library of known protein folds for automously
folding units and subdomains.
http://zebra.berkeley.edu/raft/
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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.
http://www.ks.uiuc.edu/Research/namd/
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GROMOS
A general-purpose molecular dynamics computer simulation package for the study of biomolecular
systems.
http://igc.ethz.ch/gromos/
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Bionet.software.x-plor
Archive of newsgroup for X-PLOR software for 3D macromolecular structure determination.
http://www.bio.net/hypermail/X-PLOR/
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