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Very efficient search for protein alignment—VESPA
Author(s) -
Randić M.
Publication year - 2011
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.22903
Subject(s) - adjacency list , superposition principle , computer science , generalization , order (exchange) , algorithm , displacement (psychology) , theoretical computer science , combinatorics , mathematics , psychology , mathematical analysis , finance , economics , psychotherapist
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