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Biochemistry and Molecular Biology
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- Program for bio-molecular modeling, particularly for molecular graphics and dynamics with implicit and explicit water models.
- A general purpose molecular mechanics and molecular dynamics package with the capability to compute free-energy changes.
- 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.
- 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 molecular dynamics simulation package. Offered free of charge under an academic licence to scientists pursuing research of a non-commercial nature.
- 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.
Highlights of Biochemistry
- 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
- 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.
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.
- Public domain suite of programs to aid in the modeling of protein three-dimensional structures. Tested on Linux and Unix.
- 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.
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