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Program for bio-molecular modeling, particularly for molecular graphics and dynamics with implicit and explicit water models.
Program for creating molecular models, molecular mechanics simulations and development of the force fields by quantum chemical methods.
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.
Visualization of physico-chemical structures in VML, from research at the Universities of Stuttgart and Erlangen in Nürnberg, Germany.
A parallel program for molecular dynamics simulations of biomolecules.
It is a distributed computing project which studies protein folding, misfolding, aggregation, and related diseases.
GrAfSS: Graph Theoretic Applications for Structure Searching
Graph theoretic methods for the analysis of structural relationships in biological macromolecules.
A molecular dynamics package primarily designed for biomolecular systems such as proteins and lipids. It is a free software.
A general-purpose molecular dynamics computer simulation package for the study of biomolecular systems.
The Jalview Internal PDB Viewer
Used to visualize three dimensional structure of macromolecules, using protein data bank format for atom coordinates.
Jay Ponder Lab
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.
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.
Folding simulations for fusion peptides, proteins and RNA with aim of predicting structure from genome by research at Stanford University, California.
Prion Helical Wheels
Java applet to illustrate alpha-helices, using a traditional helical wheel. Output as Postscript, JPEG, GIF or PICT.
Protein structure-function software in multiple modules, maintained at the University of Wisconsin, Madison.
SWISS-MODEL is an Automated Protein Modelling Server running at the GlaxoWellcome Experimental Research in Geneva, Switzerland.
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.
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.
Forum for 3D macromolecular structure determination. Includes links to other Biosci/Bionet newsgroups, maintained at Indiana University, Bloomington.
(Yet Another Scientific Artificial Reality Application) is an interactive real-time molecular dynamics program.
ZMM Software Inc.
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.
Last update:April 21, 2016 at 6:24:07 UTC