Class, Architecture, Topology Homology

CATH Class, architecture, topology, homologous superfamily hierarchical classi-... 

FIGURE 2 The class, architecture, topology, homology (CATH) classification of a protein. SOURCE Department of Biochemistry and Molecular Biology, University College, London. This figure can be viewed in color at . 

CATH Class, Architecture, Topology, Homology semiautomatic classification of proteins http //www.biochem.ucl.ac.uk/bsm/cath... 

The SCOP database is curated manually, with the objective of placing proteins in the correct evolutionary framework based on conserved structural features. Two similar enterprises, the CATH (class, architecture, topology, and homologous superfamily) and FSSP (/old classification based on structure-structure alignment of proteins) databases, make use of more automated methods and can provide additional information. 

Templates can be selected using the target sequence as a query for searching protein structure databases [e.g. Brookhaven Protein Data Bank (PDB) http / /www.rcsb.org/pdb/index.html Structural Classification of Proteins (SCOP) scop.mrc-lmb.cam.ac.uk/scop/ DALI www2.ebi.ac.uk/dali/ Class, Architecture, Topology and Homologous superfamily classification at CATH www.biochem.ucl.a-c.uk/bsm/cath/). 

Contains -18,000 domains organized according to then class, architecture, topology, and homologous supeifamilies. 

Thus the architecture refers to the overall shape of the protein, whereas the topology or fold group describes the relative orientations of the secondary smictures in 3D and the order in which they are connected. The Class level is derived automatically, while the architecture is assigned manually. The assignments of structures to topology families and homologous superfamilies are made by sequence and structure comparisons. Four levels are added in the hierarchical matches. They are ... 

CATH is a protein structure classification in which protein domains are clustered at four major levels class (C), architecture (A), topology (T), and homologous superfamily (H), each of which are described below. CATH uses a semiautomatic classification procedure that filters out nonprotein, models, and Coj-only structures from the PDB. Only crystal structures solved to resolution better than 3.0 A are considered, together with all NMR structures. The latest update of CATH, v2.5.1, was released January 28, 2004 and includes 48,391 domains. 

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