Title: Structure based alignment and clustering of proteins (STRALCP)

Abstract

Disclosed are computational methods of clustering a set of protein structures based on local and pair-wise global similarity values. Pair-wise local and global similarity values are generated based on pair-wise structural alignments for each protein in the set of protein structures. Initially, the protein structures are clustered based on pair-wise local similarity values. The protein structures are then clustered based on pair-wise global similarity values. For each given cluster both a representative structure and spans of conserved residues are identified. The representative protein structure is used to assign newly-solved protein structures to a group. The spans are used to characterize conservation and assign a "structural footprint" to the cluster.

Inventors:

Zemla, Adam T.; Zhou, Carol E.; Smith, Jason R.; Lam, Marisa W.

Issue Date:

Tue Jun 18 00:00:00 EDT 2013

Research Org.:

Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)

Sponsoring Org.:

USDOE

OSTI Identifier:

1084076

Patent Number(s):

8467971

Application Number:

11/890,863

Assignee:

Lawrence Livermore National Security, LLC (Livermore, CA)

Patent Classifications (CPCs):

G - PHYSICS G01 - MEASURING G01N - INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES

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

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G - PHYSICS G01 - MEASURING G01N - INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES

G01N33/6803 - {General methods of protein analysis not limited to specific proteins or families of proteins}

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

G16B15/00 - ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
G16B30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
G16B30/10 - Sequence alignment

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DOE Contract Number:  

W-7405-ENG-48

Resource Type:

Patent

Country of Publication:

United States

Language:

English

Subject:

59 BASIC BIOLOGICAL SCIENCES