Finding local structural similarities among families of unrelated protein structures: a generic non-linear alignment algorithm

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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. 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.
Original languageUndefined/Unknown
Pages (from-to)341–355
JournalProteins
Volume34
Issue number3
DOIs
Publication statusPublished - 1999
MoE publication typeA1 Journal article-refereed

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