Protein structure classifications

Department of Computer Science and Genome Center, University of California, Davis, California 

Reviews in Computational Chemistry, Volume 22 edited by Kenny B. Lipkowitz, Thomas R. Cundari, and Valerie J. Gillet Copyri t 2006 WUey-VCH, John Wiley Sons, Inc. 

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Protein Motifs Are the Basis for Protein Structural Classification... 

C. Hadley and D.T. Jones. 1999. A systematic comparison of protein structure classification SCOP, CATH and FSSP Structure Fold. Des. 7 1099-1112. (PubMed)... 

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Hadley, C. and D. T. Jones, A systematic comparison of protein structure classifications SCOP, CATH and FSSP. Structure Fold Des, 1999. 7(9) p. 1099-112. 

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Murzin, A. G., Brenner, S. E., Hubbard, T., and Chothia, C., 1995. SCOP A structural classification of proteins database for the investigation of sequences and structures./. Mol. Biol 247 536-540. Hadley, C., and Jones, D. T., 1999. A systematic comparison of protein structure classification SCOP, CATH and FSSP. Structure Fold. Des. 7 1099-1112. 

CATH Protein structure classification database http //www.biochem.ucl.ac. uk/bsm/cath/... 

SCOP Murzin s database of protein structure classification http //scop.mrc-lmb.cam.ac. uk.scop/... 

Many proteins share structural similarities due to the evolutionary process involving substitutions, insertions and deletions in amino add sequences. Consequently protein structures can be characterized according to their connnon substructures (supersecondary structures, e.g. motifs, domains). For proteins with conserved functions, the structural environments of critical active site residues are also conserved. In an attempt to better understand seqnence-structuie relationships and the underlying evolutionary processes that give rise to different fold famihes, a variety of structure classification schemes have been established. Analyses of the 3D structures archived in PDB generate various databases for the specification/search of characteristic substructures and protein structure classifications (Table 16.6). 

FSSP Protein structure classification http // www.bk>info.biocenter.helsinki.fi 8080/ dali/index.html... 

Topology, and Homologous (CATH) superfamilies classification and the domain classification based on the Distance ALIgnment (DALI) algorithm. Finally, the tutorial concludes with a discussion of the future of protein structure classifications. 

All current structural classification methods are based on the same scheme Protein structures are first divided into discrete, globular domains, which are then classified at the levels of (1) class, (2) folds, (3) superfa-milies, and (4) families. The differences among existing schemes come from the methods that define the domains and the procedures that classify. After reviewing the terms that define a classification, the three main protein structure classifications available, SCOP, CATH, and the DALI Domain Dictionary (DDD), will be described. Links to these databases and related services are listed in Table 7. 

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