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Title: Local-global alignment for finding 3D similarities in protein structures

Abstract

A method of finding 3D similarities in protein structures of a first molecule and a second molecule. The method comprises providing preselected information regarding the first molecule and the second molecule. Comparing the first molecule and the second molecule using Longest Continuous Segments (LCS) analysis. Comparing the first molecule and the second molecule using Global Distance Test (GDT) analysis. Comparing the first molecule and the second molecule using Local Global Alignment Scoring function (LGA_S) analysis. Verifying constructed alignment and repeating the steps to find the regions of 3D similarities in protein structures.

Inventors:
 [1]
  1. Brentwood, CA
Publication Date:
Research Org.:
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1027116
Patent Number(s):
8,024,127
Application Number:
10/782,061
Assignee:
Lawrence Livermore National Security, LLC (Livermore, CA)
DOE Contract Number:  
W-7405-ENG-48
Resource Type:
Patent
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Zemla, Adam T. Local-global alignment for finding 3D similarities in protein structures. United States: N. p., 2011. Web.
Zemla, Adam T. Local-global alignment for finding 3D similarities in protein structures. United States.
Zemla, Adam T. Tue . "Local-global alignment for finding 3D similarities in protein structures". United States. https://www.osti.gov/servlets/purl/1027116.
@article{osti_1027116,
title = {Local-global alignment for finding 3D similarities in protein structures},
author = {Zemla, Adam T},
abstractNote = {A method of finding 3D similarities in protein structures of a first molecule and a second molecule. The method comprises providing preselected information regarding the first molecule and the second molecule. Comparing the first molecule and the second molecule using Longest Continuous Segments (LCS) analysis. Comparing the first molecule and the second molecule using Global Distance Test (GDT) analysis. Comparing the first molecule and the second molecule using Local Global Alignment Scoring function (LGA_S) analysis. Verifying constructed alignment and repeating the steps to find the regions of 3D similarities in protein structures.},
doi = {},
journal = {},
number = ,
volume = ,
place = {United States},
year = {2011},
month = {9}
}

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Works referenced in this record:

Comparative genomics tools applied to bioterrorism defence
journal, January 2003


Optimum superimposition of protein structures: ambiguities and implications
journal, April 1996


Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
journal, September 1998

  • Shindyalov, I. N.; Bourne, P. E.
  • Protein Engineering Design and Selection, Vol. 11, Issue 9
  • DOI: 10.1093/protein/11.9.739

LGA: a method for finding 3D similarities in protein structures
journal, July 2003


ProSup: a refined tool for protein structure alignment
journal, November 2000

  • Lackner, Peter; Koppensteiner, Walter A.; Sippl, Manfred J.
  • Protein Engineering, Design and Selection, Vol. 13, Issue 11
  • DOI: 10.1093/protein/13.11.745

Protein Structure Prediction in Structure Based Drug Design
journal, March 2004

  • Takeda-Shitaka, Mayuko; Takaya, Daisuke; Chiba, Chieko
  • Current Medicinal Chemistry, Vol. 11, Issue 5
  • DOI: 10.2174/0929867043455837

Processing and evaluation of predictions in CASP4
journal, January 2001

  • Zemla, Adam; Venclovas, ?eslovas; Moult, John
  • Proteins: Structure, Function, and Genetics, Vol. 45, Issue S5
  • DOI: 10.1002/prot.10052

Protein structure prediction methods for drug design
journal, January 2000


The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models
journal, January 2004


Protein Structure Comparison by Alignment of Distance Matrices
journal, September 1993