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Automated assignment of SCOP and CATH protein structure classifications from FSSP scores
Author(s) -
Getz Gad,
Vendruscolo Michele,
Sachs David,
Domany Eytan
Publication year - 2002
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.1176
Subject(s) - computer science , function (biology) , sequence (biology) , data mining , algorithm , artificial intelligence , pattern recognition (psychology) , biology , genetics
We present an automated procedure to assign CATH and SCOP classifications to proteins whose FSSP score is available. CATH classification is assigned down to the topology level, and SCOP classification is assigned to the fold level. Because the FSSP database is updated weekly, this method makes it possible to update also CATH and SCOP with the same frequency. Our predictions have a nearly perfect success rate when ambiguous cases are discarded. These ambiguous cases are intrinsic in any protein structure classification that relies on structural information alone. Hence, we introduce the “twilight zone for structure classification.” We further suggest that to resolve these ambiguous cases, other criteria of classification, based also on information about sequence and function, must be used. Proteins 2002;46:405–415. © 2002 Wiley‐Liss, Inc.