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Title: Method for protein structure alignment

Abstract

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.

Inventors:
; ; ;
Issue Date:
Research Org.:
Stanford Univ., CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1175252
Patent Number(s):
6859736
Application Number:
09/825,441
Assignee:
The Board of Trustees of the Lealand Stanford Junior University
Patent Classifications (CPCs):
G - PHYSICS G16 - INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS G16B - BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
DOE Contract Number:  
AC03-76SF00515
Resource Type:
Patent
Country of Publication:
United States
Language:
English
Subject:
60 APPLIED LIFE SCIENCES

Citation Formats

Blankenbecler, Richard, Ohlsson, Mattias, Peterson, Carsten, and Ringner, Markus. Method for protein structure alignment. United States: N. p., 2005. Web.
Blankenbecler, Richard, Ohlsson, Mattias, Peterson, Carsten, & Ringner, Markus. Method for protein structure alignment. United States.
Blankenbecler, Richard, Ohlsson, Mattias, Peterson, Carsten, and Ringner, Markus. Tue . "Method for protein structure alignment". United States. https://www.osti.gov/servlets/purl/1175252.
@article{osti_1175252,
title = {Method for protein structure alignment},
author = {Blankenbecler, Richard and Ohlsson, Mattias and Peterson, Carsten and Ringner, Markus},
abstractNote = {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.},
doi = {},
journal = {},
number = ,
volume = ,
place = {United States},
year = {2005},
month = {2}
}

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Works referenced in this record:

Molecular docking to ensembles of protein structures 1 1Edited by B. Honig
journal, February 1997


A soft, mean-field potential derived from crystal contacts for predicting protein-protein interactions
journal, November 1998


A unified treatment of track reconstruction and particle identification
journal, July 1994


Deformable templates — revisited and extended — with an OOP implementation
journal, July 1994