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Method for protein structure alignment

United States Patent

February 22, 2005
View the Complete Patent at the US Patent & Trademark Office
SLAC National Accelerator Laboratory - Visit the Technology Transfer Website
This invention provides a method for protein structure alignment. More particularly, the present invention provides a method for identification, classification and prediction of protein structures. The present invention involves two key ingredients. First, an energy or cost function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. Second, a minimization of the energy or cost function by an iterative method, where in each iteration (1) a mean field method is employed for the assignment variables and (2) exact rotation and/or translation of atomic coordinates is performed, weighted with the corresponding assignment variables.
Blankenbecler; Richard (Stanford, CA), Ohlsson; Mattias (Lund, SE), Peterson; Carsten (Lund, SE), Ringner; Markus (Lund, SE)
The Board of Trustees of the Lealand Stanford Junior University (Stanford, CA)
09/ 825,441
April 2, 2001
STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT This invention was supported in part by grant number DE-AC03-76SF00515 from the U.S. Department of Energy. The U.S. Government has certain rights in the invention.