The Structure Classification of Proteins SCOP

SCOP is a hierarchic classification with four major levels classes, folds, superfamilies, and families. As recognized by the authors of SCOP, the exact 

At the top of the SCOP hierarchy are 11 different classes alpha, beta, alpha and beta (a/p), alpha plus beta (a + p), multidomain proteins, membrane and cell-surface proteins, small proteins, coiled coil proteins, low-resolution protein structures, peptides, and designed proteins. Note that only the first seven classes are true classes. The remaining ones serve as place holders for protein domains that cannot (yet) be classified among the major classes and are maintained in SCOP for the sake of completeness and compatibility with the PDB. 

In each SCOP class, proteins are clustered into groups based on their structure similarity. Each cluster is referred to by SCOP as a fold. Proteins share a common fold if they have the same major secondary structures in the same arrangement and with the same topological connections. Proteins with the same fold may differ at the level of their peripheral elements, which can include secondary structures and turn regions. Note that these peripheral elements can represent up to 50% of the structure. Proteins catalogued together in the same fold may have no common evolutionary origin. 

SCOP superfamilies identify probable common evolutionary origin. Proteins whose sequences have low similarities, but that share the same fold and have similar functions, suggest that a common evolutionary origin is probable. 

Proteins clustered together into families are clearly evolutionary related. The sequences of two proteins of the same family often have a residue identity greater than 30%. In some cases, a high sequence identity is not needed to affirm common origin many globins, for example, form a family, even though some members of that family have a sequence identity of only 15%. 

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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/). 

A classification system, such as Structural Classification of Proteins (SCOP) (Lesk and Chothia, 1984 Anreeva et al, 2004) categorizes structure domains based on secondary structural elements within a protein into a structure (made up primarily from a helices), P structure (made up primarily from p strands), a/p structure (comprised of primarily p strands alternating with a helices), a -i- p structure (comprised of a mixture of isolated a helices and P strands) and others. In this classification (Brenner et al., 1996), only the core of the domain is considered. Therefore it is possible for an all-a structure to have a very small amount of p strand outside the a-helical core. Similarly an aU-P protein may have a small presence of a or 3io helix. The SCOP (http //scop. mrc-lmb.cam.ac.uk/scop/) can be summarized as followings ... 

The Stractural Classification of Proteins (SCOP) database describes structural and evolutionary relationships between proteins of known structure (Lesk and Chothia, 1984 ... 

Murzin A G, S E Brenner, T Hubbard and C Chothia 1995. SCOP A Structural Classification of Proteins Database for the Investigation of Sequences and Structures. Journal of Molecular Biology 247 536-540. 

FIGURE 4-22 Organization of proteins based on motifs. Shown here are just a small number of the hundreds of known stable motifs. They are divided into four classes all a, all /3, all3, and a + /3. Structural classification data from the SCOP (Structural Classification of Proteins) database (http //scop.mrc-lmb.cam.ac.uk/scop) are also provided. The PDB identifier is the unique number given to each structure archived in the Protein Data Bank (www.rcsb.org/pdb). The a//3 barrel, shown in Figure 4-21, is another particularly common a/fS motif. 

PALI (Phylogeny and Alignment of Homologous Protein Domains) Database. The PALI (v 2.6) database provides three-dimensional structure-based sequence alignments for homologous proteins of known three-dimensional structure (24-26). The protein families have been derived from the SCOP (Structural Classification of Proteins) database (27). There are 2,518 protein families, and using more than one sequence as reference, 37,986 profiles have been generated. 

Murzin AG, Brennerm SE, Hubbard T et al (1995) SCOP a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247 536-540... 

Hubbard, T. J., et al., SCOP, Structural Classification of Proteins database applications to evaluation of the effectiveness of sequence alignment methods and statistics of protein structural data. Acta Crystallogr D Biol Crystallogr, 1998. 54(1 (Pt 6)) p. 1147-54. 

The protein 3D stmcture database http //www.rcsb.org/ Structural classifications of proteins http //scop.mrclmb.cam.ac. 

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. 

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