Automated assignment of SCOP and CATHprotein

protein structure classi cations from FSSP scores. Gad Getz1, Michele Vendruscolo2, David Sachs3 and Eytan Domany1 1 Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel 2 Oxford Centre for Molecular Sciences, New Chemistry Laboratory South Parks Road, OX1 3QT Oxford, UK 3 Department of Physics, Princeton University Princeton NJ 08544-1117, USA Abstract We present an automated procedure to assign CATH and SCOP classi cations to proteins whose FSSP score is available. CATH classi cation is assigned down to the topology level and SCOP classi cation 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 classi cation, which relies on structural information alone. Hence, we introduce the notion of \twilight zone for structure classi cation". We further suggest that in order to resolve these ambiguous cases other criteria of classi cation, based also on information about sequence and function, must be used.