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Keywords:

  • protein alignment;
  • amino acid adjacency matrix;
  • AH matrix;
  • VESPA

Abstract

A novel approach to the problem of protein alignments is described, which in comparison with existing approaches is visibly more efficient. This approach is based on superposition of amino acid adjacency matrices of a pair of proteins, which have been modified to record the sequential order of amino acids. As a result, one obtains simultaneously all segments of the two proteins which are shifted relative to one another by one or more positions in either directions, without need of a prior exhaustive search for an alignment that included unproductive directions and unknown displacement steps. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2012