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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