Automated assignment of SCOP and CATH protein structure classification from FSSP scores

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 to the fold level. As 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, which relies on structural information alone. Hence, we introduce the notion of “twilight zone for structure classification”. We further suggest that in order to resolve these ambiguous cases other criteria of classification, based also on information about sequence and function, must be used.