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

Gad Getz1, Michele Vendruscolo2, David Sachs3,and Eytan Domany1,

1Weizmann Institute of Science Rehovot, 76100, Israel
2Dept. of Chemistry Cambridge University, Cambrige CB2 1TN, UK

3Princeton, Princeton NJ 08544-1117, USA
 
You can find the article here: Proteins: Structure, Function and Genetics 46 (2002), 405-415
 

Abstract

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.

Original Figures and Sets (using CATH ver1.7 SCOP ver1.53)

Updated Figures (using CATH ver2.5 SCOP ver1.63)

  1. Z score matrix of PFrCs in random order
  2. Z score matrix of PFrCs ordered according to CATH
  3. Distribution of CATH topologies and SCOP folds in PCsSs
  4. Z score matrix of PFrCs+PFnotC; PFrCs ordered by CATH and PFnotC random
  5. Z score matrix of PFrCs+PFnotC; PFrCs ordered by CATH and PFnotC by our prediction
Updated sets (using CATH ver3.1 SCOP ver1.71)
 
 

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