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

The Modeling Facility is an integral part of the MT-COBRE and works closely with the NMR Facility, biophysicists, molecular biologists, chemists, computer scientists, and biochemists. The Facility is based on the rationalization of experimental data, the prediction of new empirical experiments, and the structure-based drug design of new agents (rationalization, prediction, and design).  The facility maintains state-of-the-art software and computational resources which provide equipment and expertise for a variety of modeling applications:  to facilitate structure-based drug design, drug discovery and drug development; to provide a bridge between crystallography, NMR, and other disciplines; to provide a collaborative environment for the JGBCC; to inform the Structural Biology group of advances in the field, and to implement them; to educate the Structural Biology group and others on possible enhancements to their research and to train students on “state-of-the-art” molecular modeling.  The Molecular Modeling/Computational Biology Core facility is staffed by an experienced Director (John O. Trent, Ph.D.) and a systems manager (Lei Wang, M.S.).  The Systems Manager oversees the day-to-day operation of the facility, is responsible for computer hardware and software maintenance including installation, code development, and trains individuals on use of the software and hardware.  The Director oversees all operations, consults with users on appropriate approaches, allocation of resources, and data analysis.  The Director also is responsible for initiating projects aimed at the development of novel in silico drug discovery.  The Molecular Modeling/ Computational Biology Core was created in 1999 when Dr. Trent was recruited to the James Graham Brown Cancer Center.  It started with three 4-processor servers and two graphics workstations.  As of 2007, it comprises 5 servers with a total of 110 processors, 6 graphics workstations, 8 PC/Macs, and a 3,500-processor distributed computing grid.  This massive grid, probably the largest network in the country, is required for searches involving millions of potential drug structures.  The core has evolved into a highly collaborative center that provides expertise and resources not available elsewhere at the UofL.  A number of significant “firsts” have been reported through work supported by the Molecular Modeling Core.  This work has resulted in more than 41 publications including four front cover illustrations