Top : Science : Biology : Biochemistry and Molecular Biology : Biomolecules :
Software
Websites
Archive of newsgroup for X-PLOR software for 3D macromolecular structure determination.
site exerpt
The X-plor Archives Send comments to us at archive@iubio.bio.indiana.edu...Rapid Autonomous Fragment Test: interface to search library of known protein folds for automously folding units and subdomains.
http://zebra.berkeley.edu/raft/
A program to perform molecular dynamics simulations on parallel as well as on sequential computers.
site exerpt
EGO A Program for Efficient Parallel Molecular Dynamics O is a program to perform molecular dynamics simulations on parallel as well as on sequential computers. Supported parallel machines include the Hitachi SR8000, CRAY-T3E, IBM-SP2, Fujitsu VPP700, Parsytec-CC under PARIX and inhomogeneous clusters of UNIX workstations under PVM or...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
"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/
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.
site exerpt
Ghemical Homepage A molecular modelling package released under the GNU GPL. Authors Ghemical authors (past and present, all in alphabetical order) include: Austin Acton, Michael Banck, Jean Brfort, Mike Cruz, Donald Curtis, Tommi Hassinen thassine@messi.uku.fi, Ville Heikkil, Geoff Hutchison, Jarno Huuskonen, Jan...A general purpose molecular mechanics and molecular dynamics package with the capability to compute free-energy changes.
site exerpt
The Amber Molecular Dynamics Package The bugs have magically disappeared Learn more about real Amber) Assisted Model Building with Energy Refinement Amber refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and...(Yet Another Scientific Artificial Reality Application) is an interactive real-time molecular dynamics program.
site exerpt
YASARA Yet Another Scientific Artificial Reality Application Click here to visit the new OpenGL screenshot gallery 300$ Reward if you find a program that beats YASARA in these benchmarks. Want to get a high performance cluster for free? Install the Models@Home screen- saver in your Linux/ Windows...A parallel molecular dynamics simulation package.
site exerpt
CLRC Computational Science and Engineering Department Molecular Simulation Enter text and press return Home About us Contact us Support and services Research and development Advanced research computing Atomic and molecular physics Band theory Computational engineering Computational material science Molecular simulations Numerical analysis Software engineering Quantum chemistry Events calendar...A parallel program for molecular dynamics simulations of biomolecules.
site exerpt
EGO References to the developers of EGO_VIII Development of a first version of EGO by Helmut Heller and Helmut Grubmüller was initiated by Klaus Schulten in his group at the Technical University of Munich. Development continued at the University of Illinois...A program for modeling protein docking.
http://reco3.musc.edu/gramm/
Folding simulations for fusion peptides, proteins and RNA with aim of predicting structure from genome by research at Stanford University, California.
site exerpt
Pande Group ligand binding protein design Theory and Simulation of Biological and Biomimetic Self-Assembly and Function Last modified June 25, 2004...Molecular structures are made visible, dependent on Chime scripts at the Faculty of Biology, University of Hamburg, Germany.
site exerpt
macromolecules: chime scripts Highlights of biochemistry:molecular structures made visible UHHFacultyofBiologyTeaching Stuff Highlights of Biochemistry search The examples of molecular structures shown here may only be viewed when Chime is installed as a plug-in for Netscape (4.x) or another suitable browser Besides our scripts...Visualization of physico-chemical structures in VML, from research at the Universities of Stuttgart and Erlangen in Nürnberg, Germany.
site exerpt
ChemVis Chemical Visualization on the Internet Last modified 2004-09-21...PSCAN, PMOL2Q, DBFILTER download page. Taichung, Taiwan.
http://home.pchome.com.tw/team/gentamicin/mol/mol.htm
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.
site exerpt
PDB Viewer Fast and Simple 3D Protein Viewer It allows you to model structures in a simple and easy to use application. PDB Viewer is a small viewer written as part of my Final Year University Project. It aims to provide some of the basic viewing options required...Molecular dynamics simulation programs for proteins, DNA, and RNA, including 3D viewing of molecules. Offers downloadable demonstration version, from Milpitas California.
site exerpt
Protein Dynamics,Inc. Inc the creator of the only molecular dynamics simulation program for the Macintosh. We are a software innovator focusing on the biotechnology and pharmaceutical markets. Molecular Dynamics on the Mac Moreau software can be used as a scientific or educational...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.
site exerpt
SWBIC Bioinformatics Solve mysteries using forensic techniques. DoD Biotech Resources Minority Student Resources Bioinformatics Tools Search Internet Resources Bioinformatics SWBIC Products Services Bioinformatics Tools BLAST Filter: Builds a set of related sequences by running BLAST on your DNA or protein query sequence,...Java applet to illustrate alpha-helices, using a traditional helical wheel. Output as Postscript, JPEG, GIF or PICT.
site exerpt
You must have java running to use the interactive applet. But you can use the tools below to make nice helical wheels. FAQs How can I print a helical wheel? What about the guy that discovered the alpha-helix? Java Applet...Protein structure-function software in multiple modules, maintained at the University of Wisconsin, Madison.
site exerpt
Sesame Sesame project are to develop a computing infrastructure, based on the client/server paradigm and utilizing distributed objects, to support high-throughput protein structure-function investigations. The Sesame project is made up of a number of individual modules each of which is designed...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.
site exerpt
IMB Jena Image Library of Biological Macromolecules Macromolecules is aimed at a better dissemination of information on three-dimensional biopolymer structures with an emphasis on visualization and analysis. It provides access to all structure entries deposited at the Protein Data Bank (PDB) or at the Nucleic Acid Database...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.
site exerpt
Jay Ponder Lab Home Page We are located in the recently renovated Center for Computational Biology building on the Medical School campus. Our group is primarily interested in computational chemistry, especially the development of new algorithms and their application to problems in structural biology. We...Public domain suite of programs to aid in the modeling of protein three-dimensional structures. Tested on Linux and Unix.
site exerpt
RAMP HOWTO Setting up the distribution 2.3 Using the default setup 2.4 Changing the defaults and recompiling 2.5 Using RAMBIN 2.6 Using a login shell other than tcsh 3. General issues 3.1 Command line interface 3.2 Terminology 3.3 Directory structure 3.4 Environment...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.ru.nl/whatif/
PSdb uses primary data, to relate secondary and tertiary information, for solvent accessibility, internal relative distances, and ligand interactions. Maintained at the Mellon Institute, Pittsburgh, Pennsylvania.
site exerpt
The Protein Structure Database (PSdb) Java based vizualization tool for viewing PSdb entries. PSdbView is available on-line or may be downloaded for use locally Note: Java enabled browser or local Java interpretter required) The PSdb currently consists of 1191 protein entries. More information about the...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.
site exerpt
ZMM Molecular Modeling Software for everybody, as easy to use as Rasmol M is a molecular modeling program for theoretical studies of systems of any complexity: small molecules, peptides, proteins, nucleic acids, and ligand-receptor complexes. ZMM searches optimal structures in the space of generalized coordinates: torsion angles, bond angles, bond lengths, positions...