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Finding local structural similarities among families of unrelated protein structures: A generic non‐linear alignment algorithm
Author(s) -
Lehtonen Jukka V.,
Denessiouk Konstantin,
May Alex C.W.,
Johnson Mark S.
Publication year - 1999
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/(sici)1097-0134(19990215)34:3<341::aid-prot7>3.0.co;2-z
Subject(s) - threading (protein sequence) , structural alignment , similarity (geometry) , computer science , homology (biology) , protein superfamily , algorithm , protein structure , local structure , topology (electrical circuits) , sequence alignment , mathematics , artificial intelligence , combinatorics , genetics , biology , crystallography , peptide sequence , biochemistry , chemistry , gene , image (mathematics)
Abstract We have developed a generic tool for the automatic identification of regions of local structural similarity in unrelated proteins having different folds, as well as for defining more global similarities that result from homologous protein structures. The computer program GENFIT has evolved from the genetic algorithm‐based three‐dimensional protein structure comparison program GA_FIT.1, 2 GENFIT, however, can locate and superimpose regions of local structural homology regardless of their position in a pair of structures, the fold topology, or the chain direction. Furthermore, it is possible to restrict the search to a volume centered about a region of interest (e.g., catalytic site, ligand‐binding site) in two protein structures. We present a number of examples to illustrate the function of the program, which is a parallel processing implementation designed for distribution to multiple machines over a local network or to run on a single multiprocessor computer. Proteins 1999;34:341–355. © 1999 Wiley‐Liss, Inc.