Core C: The Molecular Modeling Core - John O. Trent, Ph.D.

This state-of-the-art Molecular Modeling Facility has the capability of providing models based on structural data obtained from either X-ray crystallographic or NMR studies.  The Director, Dr. John Trent, is available on a collaborative basis to provide assistance and instruction for individual faculty members or students.  This facility is located within the James Graham Brown Cancer Center.  The Molecular Modeling Core includes a Silicon Graphics Array (39xR12000 processors with over 420 GB storage), an Origin 2000 server, three Origin 200 servers and four OCTANE graphics workstations with an O2 graphics workstation, connected through a 100bT dedicated local area network.  Molecular modeling software includes Amber 4.1, 5.0, 6.0 (Oxford Molecular), Macromodel (Columbia University), Insight II modules (MSI), Discover, Affinity, Biopolymer, Builder, as well as evaluation versions of SYBYL and UNITY.  These facilities permit ab initio, semi-empirical, and Poisson-Boltzman electrostatic calculations and the running of GAMESS, MOPAC, Delphi, Molecular Graphics and visualization packages - Grasp (Columbia University), Midas-plus, Chimera (UCSF) and DNA analysis programs (Curves).  Other programs include MC-SYM, Namot, moil-view, VMD, molekel and rasmol.  In addition to the computational resources, time on the University of Louisville IBM SP2 supercomputer (112 power3 RS6000 processors) is available.  The capabilities of the facility include techniques such as explicitly solvated molecular dynamics, homology modeling, docking, virtual screening, ESP calculations, and conformational searching.  The Molecular Modeling Core is available to all MT-COBRE investigators and provides important information on drug design and modification.