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

Zemla, Adam T

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

Patent · 20 September 2011

OSTI ID:1027116

Zemla, Adam T ^[1]

Brentwood, CA

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.

Research Organization:: Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)

Sponsoring Organization:: USDOE

DOE Contract Number:: W-7405-ENG-48

Assignee:: Lawrence Livermore National Security, LLC (Livermore, CA)

Patent Number(s):: 8,024,127

Application Number:: 10/782,061

OSTI ID:: 1027116

Country of Publication:: United States

Language:: English

References (12)

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Processing and evaluation of predictions in CASP4 Zemla, Adam; Venclovas, ?eslovas; Moult, John Proteins: Structure, Function, and Genetics, Vol. 45, Issue S5 https://doi.org/10.1002/prot.10052	journal	January 2001
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A study of quality measures for protein threading models Cristobal, Susana; Zemla, Adam; Fischer, Daniel BMC Bioinformatics, Vol. 2, Issue 1, p. 5 https://doi.org/10.1186/1471-2105-2-5	journal	January 2001
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Comparative genomics tools applied to bioterrorism defence Slezak, T. Briefings in Bioinformatics, Vol. 4, Issue 2 https://doi.org/10.1093/bib/4.2.133	journal	January 2003
Protein Structure Comparison by Alignment of Distance Matrices Holm, Liisa; Sander, Chris Journal of Molecular Biology, Vol. 233, Issue 1 https://doi.org/10.1006/jmbi.1993.1489	journal	September 1993

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