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Amber - A general purpose molecular mechanics and molecular dynamics package with the capability to compute free-energy changes.
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.
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 - "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.
Bionet.software.x-plor - Archive of newsgroup for X-PLOR software for 3D macromolecular structure determination.
CADD tools in Drug R&D - PSCAN, PMOL2Q, DBFILTER download page. Taichung, Taiwan.
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.
ChemVis - Visualization of physico-chemical structures in VML, from research at the Universities of Stuttgart and Erlangen in Nürnberg, Germany.
DL Poly - A parallel molecular dynamics simulation package.
EGO - A parallel program for molecular dynamics simulations of biomolecules.
EGO VIII - A program to perform molecular dynamics simulations on parallel as well as on sequential computers.
Folding@home - It is a distributed computing project which studies protein folding, misfolding, aggregation, and related diseases.
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.
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.
GRAMM (Global Range Molecular Matching) - A program for modeling protein docking.
GROMOS - A general-purpose molecular dynamics computer simulation package for the study of biomolecular systems.
Helical Wheels - Java applet to illustrate alpha-helices, using a traditional helical wheel. Output as Postscript, JPEG, GIF or PICT.
Highlights of Biochemistry - Molecular structures are made visible, dependent on Chime scripts at the Faculty of Biology, University of Hamburg, Germany.
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 - Folding simulations for fusion peptides, proteins and RNA with aim of predicting structure from genome by research at Stanford University, California.
PDB Viewer - 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.
Protein Dynamics, Inc. - Molecular dynamics simulation programs for proteins, DNA, and RNA, including 3D viewing of molecules. Offers downloadable demonstration version, from Milpitas California.
RAFT - Rapid Autonomous Fragment Test: interface to search library of known protein folds for automously folding units and subdomains.
Sesame Project - Protein structure-function software in multiple modules, maintained at the University of Wisconsin, Madison.
Southwest Biotechnology and Informatics Center - 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.
SWISS-MODEL - SWISS-MODEL is an Automated Protein Modelling Server running at the GlaxoWellcome Experimental Research in Geneva, Switzerland.
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 - 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.
YASARA - (Yet Another Scientific Artificial Reality Application) is an interactive real-time molecular dynamics program.
Related Categories:
Science > Biology > Biochemistry and Molecular Biology > Biomolecules > Proteins and Enzymes > Structure
Science > Biology > Biochemistry and Molecular Biology > Software
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