Software Biomolecules Biochemistry and Molecular Biology

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.

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GrAfSS: Graph Theoretic Applications for Structure Searching - Graph theoretic methods for the analysis of structural biochemistry and molecular biomolecules biology relationships in biological macromolecules.
B: On-line Molecular Modeling - "B" (formerly known as Biomer) is a Java-based software molecular modeling software program for small organic molecules software and biopolymers. Supports software nucleic acids (DNA/RNA), polypeptides, software polysaccharides, the AMBER force field, geometry software optimization, simulated software ann
IMB Jena Image Library of Biological Macromolecules - Resource for visualization and analysis of 3D-biopolymer structures; proteins, nucleic software acids, carbohydrates, and small molecule ligands. Combines experimental and computer software generated models, maintained in Germany.
Genoscience - Genmol is a 3D molecular modeling software for software measuring resistance/affinity between a ligand and a target, software used for disease management and drug discovery. Details software of company in Marseille, France.
ZMM Software Inc. - Modeling tool for theoretical studies, employing molecular mechanics software approach in biochemistry and molecular biology combination with Monte Carlo energy minimization software algorithm. Downloads on secure biochemistry and molecular biology server, and contacts in software Flamborough, Ontario.
Highlights of Biochemistry - Molecular structures are made visible, dependent on Chime scripts at software the Faculty of Biology, University of Hamburg, Germany.
SWISS-MODEL - SWISS-MODEL is an Automated Protein Modelling Server running at the biochemistry and molecular biology GlaxoWellcome Experimental Research in Geneva, Switzerland.
TINKER - A free molecular modeling package for molecular mechanics and dynamics, biomolecules with some special features for biopolymers. Distributed as source code biomolecules and as binaries for Windows9x, Linux and Mac.
Bioinformatics Tools - Sequence analysis tools including protein classification with the software assistance of predicted secondary structure and sequence format software tools, available from the Molecular Biology Program at software New Mexico State University.
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.
X-plor Archives - Forum for 3D macromolecular structure determination. Includes links biomolecules to other Biosci/Bionet newsgroups, maintained at Indiana University, biomolecules Bloomington.
Ascalaph DNA - Program for creating models of nucleic acids and biomolecules their complexes with low-molecular-weight and protein ligands.
WhatIf - Protein structure analysis software for Linux, SGI/IRIX, Windows software NT. Performs biomolecules mutant prediction, structure verification, homology modeling software and molecular visualization. Links biomolecules to the documentation in software HTML. Commercial software.
NAMD - A parallel, object-oriented molecular dynamics code designed for software high-performance simulation of large biomolecular systems. NAMD is software distributed free of charge and includes source code.
BioAdviser - Package for displaying, analyzing, and manipulating 3D structures of biological software macromolecules, with special emphasis on the study of proteins and software enzymes. Includes links to other products by FQS Poland, in software Krakow.
Prion Helical Wheels - Java applet to illustrate alpha-helices, using a traditional biochemistry and molecular software biology helical wheel. Output as Postscript, JPEG, GIF or biochemistry and software molecular biology PICT.
CHARMM - A program for macromolecular dynamics and mechanics. It biomolecules performs standard molecular dynamics in many different ensembles biomolecules (e.g., NVE, NVT, NPT) using state-of-the-art algorithms for biomolecules timestepping, long range force calculation and periodic images.
RAMP - Public domain suite of programs to aid in the modeling of protein three-dimensional structures. Tested on Linux and Unix.
ChemVis - Visualization of physico-chemical structures in VML, from research at the software Universities of Stuttgart and Erlangen in Nürnberg, Germany.
Gromacs - A molecular dynamics package primarily designed for biomolecular systems such software as proteins and lipids. It is a free software.
GROMOS - A general-purpose molecular dynamics computer simulation package software for the biomolecules study of biomolecular systems.
Ghemical - An easy-to-use molecular editor and modeling package with biomolecules all-atoms molecular biomolecules mechanics, reduced protein models and links biomolecules to many common chemistry biomolecules programs. Ghemical is released biomolecules under the GNU GPL and includes biomolecules source code.
AutoDock - A suite of automated docking tools. It is software designed to predict how small flexible molecules, such software as substrates or drug candidates, bind to a software receptor of known 3D structure.
Sesame Project - Protein structure-function software in multiple modules, maintained at biomolecules the University of Wisconsin, Madison.
EGO VIII - A program to perform molecular dynamics simulations on parallel as biochemistry and molecular biology well as on sequential computers.
Protein Structure Database - PSdb uses primary data, to relate secondary and biochemistry and molecular biology tertiary information, for solvent accessibility, internal relative distances, biochemistry and molecular biology and ligand interactions. Maintained at the biochemistry and molecular biology Mellon Institute, Pittsburgh, Pennsylvania.
Pande Group - Folding simulations for fusion peptides, proteins and RNA biochemistry and molecular software biology with aim of predicting structure from genome by biochemistry and software molecular biology research at Stanford University, California.
EGO - A parallel program for molecular dynamics simulations of software biomolecules.
Folding@home - It is a distributed computing project which studies biochemistry and molecular biochemistry and molecular biology biology protein folding, misfolding, aggregation, and related diseases.
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.
Amber - A general purpose molecular mechanics and molecular dynamics package with the capability to compute free-energy changes.
Jay Ponder Lab - Graphical user interface to suites of molecular modeling biochemistry and molecular software biology tools, providing an integrated environment for engineering applications. biochemistry and software molecular biology Contacts for the group at Washington University School biochemistry software and molecular biology of Medicine in Saint Louis, Missouri.
YASARA - (Yet Another Scientific Artificial Reality Application) is an biochemistry and molecular biomolecules biology interactive real-time molecular dynamics program.

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