Directory of Software Resources

Home > Science > Biology > Biochemistry and Molecular Biology > Biomolecules > Software

Subcategories

• Nucleic Acids
• Proteins

Resources in This Category

• Abalone

  http://www.biomolecular-modeling.com/Abalone/
  Program for bio-molecular modeling, particularly for molecular graphics and dynamics with implicit and explicit water models.

• Ascalaph Designer

  http://www.biomolecular-modeling.com/Ascalaph/Ascalaph_Designer.html
  Program for creating molecular models, molecular mechanics simulations and development of the force fields by quantum chemical methods.

• AutoDock

  http://autodock.scripps.edu/
  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

  http://casegroup.rutgers.edu/Biomer/
  "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.

• ChemVis

  http://www2.chemie.uni-erlangen.de/projects/ChemVis/
  Visualization of physico-chemical structures in VML, from research at the Universities of Stuttgart and Erlangen in Nürnberg, Germany.

• EGO

  http://heller.userweb.mwn.de/ego/
  A parallel program for molecular dynamics simulations of biomolecules.

• Folding@home

  http://folding.stanford.edu/
  It is a distributed computing project which studies protein folding, misfolding, aggregation, and related diseases.

• GrAfSS: Graph Theoretic Applications for Structure Searching

  http://mfrlab.org/grafss/
  Graph theoretic methods for the analysis of structural relationships in biological macromolecules.

• Gromacs

  http://www.gromacs.org/
  A molecular dynamics package primarily designed for biomolecular systems such as proteins and lipids. It is a free software.

• Jay Ponder Lab

  http://dasher.wustl.edu/
  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.

• NAMD

  http://www.ks.uiuc.edu/Research/namd/
  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.

• Pande Group

  http://pande.stanford.edu/
  Folding simulations for fusion peptides, proteins and RNA with aim of predicting structure from genome by research at Stanford University, California.

• Prion Helical Wheels

  http://www.mad-cow.org/~tom/helical_wheel.html
  Java applet to illustrate alpha-helices, using a traditional helical wheel. Output as Postscript, JPEG, GIF or PICT.

• Sesame Project

  http://www.sesame.wisc.edu/
  Protein structure-function software in multiple modules, maintained at the University of Wisconsin, Madison.

• The Jalview Internal PDB Viewer

  http://www.jalview.org/help/html/features/pdbviewer.html
  Used to visualize three dimensional structure of macromolecules, using protein data bank format for atom coordinates.

• TINKER

  http://dasher.wustl.edu/tinker/
  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.

• WhatIf

  http://www.cmbi.ru.nl/whatif/
  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.

• X-plor Archives

  http://www.bio.net/hypermail/X-PLOR/
  Forum for 3D macromolecular structure determination. Includes links to other Biosci/Bionet newsgroups, maintained at Indiana University, Bloomington.

• YASARA

  http://www.yasara.org/
  (Yet Another Scientific Artificial Reality Application) is an interactive real-time molecular dynamics program.

• ZMM Software Inc.

  http://www.zmmsoft.com/
  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.

Related Categories

• Home > Science > Biology > Biochemistry and Molecular Biology > Biomolecules > Proteins and Enzymes > Structure
• Home > Science > Biology > Biochemistry and Molecular Biology > Software
• Home > Science > Biology > Bioinformatics > Online Services
• Home > Science > Chemistry > Software
• Home > Science > Physics > Crystallography > Software

 

Home > Science > Biology > Biochemistry and Molecular Biology > Biomolecules > Software

 

---

 

Thanks to DMOZ, which built a great web directory for nearly two decades and freely shared it with the web. About us