Folding@home - It is a distributed computing project which studies protein folding, misfolding, aggregation, and related diseases. 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. X-plor Archives - Forum for 3D macromolecular structure determination. Includes links to other Biosci/Bionet newsgroups, maintained at Indiana University, Bloomington. 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. YASARA - (Yet Another Scientific Artificial Reality Application) is an interactive real-time molecular dynamics program. ChemVis - Visualization of physico-chemical structures in VML, from research at the Universities of Stuttgart and Erlangen in Nürnberg, Germany. Sesame Project - Protein structure-function software in multiple modules, maintained at the University of Wisconsin, Madison. 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. 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. 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. Gromacs - A molecular dynamics package primarily designed for biomolecular systems such as proteins and lipids. It is a free software. Prion Helical Wheels - Java applet to illustrate alpha-helices, using a traditional helical wheel. Output as Postscript, JPEG, GIF or PICT. GrAfSS: Graph Theoretic Applications for Structure Searching - Graph theoretic methods for the analysis of structural relationships in biological macromolecules. The Jalview Internal PDB Viewer - Used to visualize three dimensional structure of macromolecules, using protein data bank format for atom coordinates. Abalone - Program for bio-molecular modeling, particularly for molecular graphics and dynamics with implicit and explicit water models. Ascalaph Designer - Program for creating molecular models, molecular mechanics simulations and development of the force fields by quantum chemical methods. 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. EGO - A parallel program for molecular dynamics simulations of biomolecules. AutoDock - 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. Pande Group - Folding simulations for fusion peptides, proteins and RNA with aim of predicting structure from genome by research at Stanford University, California.