software

    Top: Science: Biology: Biochemistry_and_Molecular_Biology: Biomolecules: Software:

• Top/Science/Biology/Biochemistry and Molecular Biology/Biomolecules/Proteins and Enzymes/Structure
• Top/Science/Biology/Biochemistry and Molecular Biology/Software
• Top/Science/Chemistry/Software
• Top/Science/Biology/Bioinformatics/Online Services

• - 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.
  
• - It is a distributed computing project which studies protein folding, misfolding, aggregation, and related diseases.
  
• - A general-purpose molecular dynamics computer simulation package for the study of biomolecular systems.
  
• - Folding simulations for fusion peptides, proteins and RNA with aim of predicting structure from genome by research at Stanford University, California.
  
• - Java applet to illustrate alpha-helices, using a traditional helical wheel. Output as Postscript, JPEG, GIF or PICT.
  
• - Molecular structures are made visible, dependent on Chime scripts at the Faculty of Biology, University of Hamburg, Germany.
  
• - A program to perform molecular dynamics simulations on parallel as well as on sequential computers.
  
• - Molecular dynamics simulation programs for proteins, DNA, and RNA, including 3D viewing of molecules. Offers downloadable demonstration version, from Milpitas California.
  
• - A parallel program for molecular dynamics simulations of biomolecules.
  
• - A program for modeling protein docking.
  
• - 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.
  
• - Archive of newsgroup for X-PLOR software for 3D macromolecular structure determination.
  
• - 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.
  
• - SWISS-MODEL is an Automated Protein Modelling Server running at the GlaxoWellcome Experimental Research in Geneva, Switzerland.
  
• - 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.
  
• - A general purpose molecular mechanics and molecular dynamics package with the capability to compute free-energy changes.
  
• - Visualization of physico-chemical structures in VML, from research at the Universities of Stuttgart and Erlangen in Nürnberg, Germany.
  
• - 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.
  
• - A parallel molecular dynamics simulation package.
  
• - 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.
  
• - 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.
  
• - (Yet Another Scientific Artificial Reality Application) is an interactive real-time molecular dynamics program.
  
• - Public domain suite of programs to aid in the modeling of protein three-dimensional structures. Tested on Linux and Unix.
  
• - 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.
  
• - PSCAN, PMOL2Q, DBFILTER download page. Taichung, Taiwan.
  
• - 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.
  
• - 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.
  
• - 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.
  
• - Rapid Autonomous Fragment Test: interface to search library of known protein folds for automously folding units and subdomains.
  
• - Protein structure-function software in multiple modules, maintained at the University of Wisconsin, Madison.
  
• - "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 ann
  
• - 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.
  
• - 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.
  
• - 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.