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Automated Generation of Motif Templates in Protein Function Prediction Software ProMOL
Author(s) -
Osipovitch Mikhail,
Bernstein Herbert J.,
Craig Paul A.
Publication year - 2013
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.27.1_supplement.811.2
Subject(s) - template , motif (music) , computer science , structural motif , software , visualization , computational biology , data mining , programming language , biology , biochemistry , physics , acoustics
ProMOL, an extension for molecular visualization system PyMOL, is structure‐based protein function prediction software. ProMOL implements routines for building motif templates based on active sites of proteins of known structure and function and screening unassigned structures for presence of the motif templates. Presently, motif generation in ProMOL requires user intervention in optimization of parameters for sensitivity and selectivity. An algorithm was developed to automate motif building and testing routines of ProMOL. The algorithm uses a set of empirically derived parameters for optimization, requires little user intervention, and provides a possibility for extending the ProMOL library of motif templates at a much higher rate. Presently, the library contains 181 motif templates. As a result of automating motif building and testing routines, 388 motif templates were generated and tested against their native, known homologous, and non‐homologous structures. The automatically generated motif templates exhibited comparable performance to the existing manually generated motif templates in terms of the rates of true positive and true negative results. The research is supported by 2R15GM078077–02.