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Structure based alignment and clustering of proteins (STRALCP)

United States Patent

June 18, 2013
View the Complete Patent at the US Patent & Trademark Office
Lawrence Livermore National Laboratory - Visit the Industrial Partnerships Office Website
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.
Zemla; Adam T. (Brentwood, CA), Zhou; Carol E. (Pleasanton, CA), Smith; Jason R. (Mountain House, CA), Lam; Marisa W. (Pleasanton, CA)
Lawrence Livermore National Security, LLC (Livermore, CA)
11/ 890,863
August 7, 2007
STATEMENT REGARDING FEDERALLY FUNDED RESEARCH The United States Government has rights in this invention pursuant to Contract No. W-7405-ENG-48 between the United States Department of Energy and the University of California, for the operation of Lawrence Livermore National Laboratory.