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STOCHASTIC MOLECULAR BINDING SIMULATION

United States Patent Application

20100138205
A1
View the Complete Application at the US Patent & Trademark Office
Los Alamos National Laboratory - Visit the Technology Transfer Division Website
The invention provides methods of dynamically simulating molecular interactions between a target molecule and a plurality of ligand molecules. The ligand molecules may be presented in the model as a homogeneous set of identical ligands or as a heterogeneous set of different ligands, such as, for example, a set of structural variants of a ligand molecule. Typically, the ligand molecule will be a small organic compound, such as a drug or other small molecule, and the ligand will be a protein or a protein domain, a nucleic acid (i.e., DNA, RNA), or a biomolecular complex of proteins and/or nucleic acid molecules. Unlike all known molecular dynamics simulation methods, the invention provides ligand molecules to the simulation's interaction environment(s) in excess relative to the target molecule.
Sanbonmatsu, Kevin Y. (Santa Fe, NM), Whitford, Paul (Santa Fe, NM), Onuchic, Jose (San Diego, CA)
LOS ALAMOS NATIONAL SECURITY, LLC (Los Alamos NM)
12/ 578,433
October 13, 2009
STATEMENT AS TO RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT [0002] This invention was made with government support under Contract No. DE-AC52-06 NA 25396 awarded by the U.S. Department of Energy. The government has certain rights in the invention.