From Bioinformatics.Org Wiki
- Abalone - a GPU accelerated program for molecular dynamics simulations of proteins, DNA, ligands.
- Amber - ($) "Assisted Model Building with Energy Refinement" is a set of molecular mechanical force fields for the simulation of biomolecules and a package of molecular simulation programs which includes source code and demos
- AMMP - a modern full-featured molecular mechanics, dynamics and modeling program
- AutoDock - a suite of automated docking tools designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure
- Babel - a program designed to inter-convert a number of file formats currently used in molecular modeling
- CHARMm - ($) "Chemistry at HARvard Macromolecular Mechanics" is a versatile and widely used molecular simulation program with broad application to many-particle systems
- Friend - a bioinformatics application designed for simultaneous analysis and visualization of multiple structures and sequences of proteins and/or DNA/RNA
- GAMESS - the "General Atomic and Molecular Electronic Structure System" is a general ab initio quantum chemistry package.
- GDIS - a GTK based program for the display and manipulation of isolated molecules and periodic systems
- Ghemical - a molecular modelling package; graphical user interface is built on GTK2; both quantum-mechanical and forcefield-based methods are supported, and it is also possible to add new methods
- Gromacs - the World' s fastest molecular dynamics - and it's GPL
- Kintecus - Run chemical kinetics/fitting of catalyst reactor, and enzyme reactions
- MMTK - "Molecular Modeling Tool-Kit"
- MODELLER - comparative protein structure modeling by satisfaction of spatial restraints
- Oslet - a molecular modeling and simulation environment in Java, mainly for education
- PyMol - a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations
- TINKER - software tools for protein simulations.
- WHAT IF - a versatile protein structure analysis program that can be used for mutant prediction, structure verification, molecular graphics, etc.