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Comparison of the efficiency of evolutionary change‐based and side chain orientation‐based fold recognition potentials
Author(s) -
Vishnepolsky Boris,
Managadze Grigol,
Pirtskhalava Malak
Publication year - 2008
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/prot.21871
Subject(s) - residue (chemistry) , side chain , similarity (geometry) , chemistry , computational biology , biology , computer science , artificial intelligence , biochemistry , organic chemistry , polymer , image (mathematics)
The present article describes residue level knowledge based potential SORDIS. SORDIS incorporates the information on side‐chain orientation in relation to hydrophobic core centres, distance of residue from the globule centre and secondary structure. SORDIS has been tested and compared with widespread evolutionary change‐based substitution matrices (BLOSUM, PAM, GONNET, Johnson‐Overington, BLAJ, HSDM, and STROMA) in fold recognition experiments within the zone of weak sequence similarity (<16%). The obtained results show that the lower is the amino acid similarity between homologous pairs the higher is the performance of SORDIS in comparison with the potentials, based on the information about the evolutionary changes. Therefore, we propose that the employment of SORDIS in fold recognition can be useful. Proteins 2008. © 2008 Wiley‐Liss, Inc.