Dr. Michael K. Gilson

Ph.D. Biochemistry and Molecular Biophysics, Columbia University, 1988
M.D. Columbia University, 1989
Professor
Center for Advanced Research in Biotechnology
9600 Gudelsky Drive
Rockville, MD 20850
Telephone:  (301)-738-6217

Email:  gilson@umbi.umd.edu
Home Page: gilsonlab.umbi.umd.edu
Research:   Molecular Modeling and Computational Chemistry.

We are interested in molecular recognition, especially the noncovalent binding of small molecules by
proteins and by synthetic host molecules. The long-term goal of our research in this area is to
develop validated models and software, based upon physical chemical principles, that predict the bound conformations of noncovalent complexes and their standard free energies of binding. Such models will be of value in a range of applications, including protein-engineering, and  structure-based  drug-design.  A novel method of computing configuration integrals forms the basis of our approach to computing binding affinities, and we are also developing novel protein-ligand "docking" algorithms.

As new methods are proven, we develop software with efficient implementations and convenient user-interfaces, so that other research groups can use the methods easily.  We are currently using PYTHON to hold together subroutines and to build user interfaces with TCL/TK and Open/GL.

A related project involves establishment of a new web-accessible database with measured binding. affinities for a variety of molecular types.  It is anticipated that data will be extracted from the published literature, and also deposited directly into the database by experimentalists, via on-line forms.  Information on this project is currently available at www.sdsc.edu/DbNcB and will soon be available at the new URL www.bindingdb.org.

Extensive computational resources are available, including two SGI Octane R10000 workstations, one SGI Indigo2 R8000 workstation, three SGI Indigo2 R4400 workstations, a dual-Pentium Pro machine running Linux, and several PCs running Windows NT. We also use computers at the National Institute of Standards and Technology, including:

IBM SP2, 37 nodes.
Linux cluster with 17 333MHz Pentium II nodes
SGI Origin 2000 with 8 R10000 processors.
SGI Origin 2000 with 32 R10000 processors.
SGI Onyx with 12 R10000 processors.
SGI Onyx with 6 R10000 processors.
Five SGI Octanes with 2 R10000 processors apiece.
Dye sublimation and color laser printers.
Large-format color laser printer.
Video-preparation laboratory.
8-processor R10000 machine, two 4-processor R10000 machines, a 32-node
IBM SP2, and a CRAY C90.

Our work is funded by the National Institute of Standards and Technology (Laboratories Program,
Advanced Technology Program, Standard Reference Data Program),  the National Institutes of
Health, and the National Science Foundation.

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