Software Currently Available and Supported

Modeling

• MOE - The Molecular Operating Environment is a comprehensive software package combining High Throughput Discovery, Bioinformatics, Cheminformatics, Structure-Based Design, Protein Modeling and Simulations.
• Insight II - Insight II is a 3D graphical environment for molecular modeling. Its powerful user interface enables the seamless flow of data between a wide range of scientific applications. The Insight II environment integrates builder modules, development tools, force fields, simulation and visualization tools with tools specifically developed for applications in the life and materials sciences. Software is available for use in the core facility with modules Affinity, Biopolymer, Discover and Homology.
• Pymol - PyMOL is 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. It can also perform many other valuable tasks (such as editing PDB files) to assist you in your research.
• VMD - VMD is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer.

Molecular Dynamics

• NAMD - NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems.
• AMBER - A parallel computer program for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to elucidate the structures and energies of molecules.
• GROMACS - A versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

Protein Structure Prediction

• Stable Coil - Stable Coil is a program designed to predict the location and stability of alpha-helical coiled-coil conformations within protein sequences. The program uses experimentally derived alpha-helical propensity and stability coefficient. By summing the residue scores over a window width of 21, 28, 35 and 42, and comparing the total score to known globular and cytoskeletal coiled-coil containing sequences, the program displays the region and probability (in kcal/mol) that a particular sequence will adopt a coiled-coil conformation.