Computational Equipment

Computational resources include 36 Dell Xeon processors (2.1-3.6GHz; 3-16GB RAM) running RedHat Enterprise or CentOS Linux for molecular computation and graphics. PBS is used for job management across our multiprocessor cluster. We have more than 15 Terabytes of disk space, with daily data backups onto external drives and a dedicated laboratory firewall and switch. Peripherals include B&W and color laser printers and scanners/copiers.

Software

Our software collection includes:

• OpenEye Omega, QUACPAC, Vida, EON, ROCS, and OEChem
• Molecular mechanics packages YASARA Structure, CHARMM and MMTSB, AMBER, GROMACS, and ProFlex
• Crystallographic, modeling, and structural analysis packages Chimera, MODELLER, ProAct, ProCheck, PyMOL, Reduce, and WhatIf
• Docking tools SLIDE, AutoDock, AutoDock Vina, and GOLD
• Molecular interaction scoring by SLIDE_score, DrugScore(PDB), DrugScore(CSD), DrugScoreX, and LigScore
• MATLAB and R statistical and mathematical analysis software
• Regular updates of the Protein Data Bank, Cambridge Structural Database, and CAS Registry/SciFinder
• C, C++, Python, and FORTRAN compilers and debuggers