SCOP classification system

A classification system, such as SCOP (Lesk and Chothia, 1984), categorizes structure domains based on secondary structural elements within a protein into a. structure (made up primarily from a helices), / structure (made up primarily from / strands), a// structure (comprised of primarily P strands alternating with a helices), and a + P structure (comprised of a mixture of isolated a helices and / strands). In this classification (Brenner et al, 1996 Lesk, 1991), only the core of the domain is considered. Therefore, it is possible for an all-a structure to have very small amount of p strand outside the a-helical core. Similarly, an all-/ protein may have a small presence of a or 310 helix. The SCOP (http //scop.mrc-lmb.cam.ac.uk/scop/) can be summarized as follows ... 

There are two main classification systems to organize proteins based on their structure CATH [174] and SCOP [175]. These systems are used to label training data for a number of supervised learning problems found in protein structure prediction. This problem is divided into three subproblems depending on the data... 

Inspection of the Serratia endonuclease structure reveals that its fold differs from other nucleases whose structures are known (28). In the SCOP protein classification system it is listed as the only member of its family (29) In the CATH protein classification system, it is listed as the only member of its tertiary group (20). The dimeric enzyme is almost cylindrical with overall dimensions of 30 A X 35 A X 90 A (Fig. 3). Each monomer consists of a central six-stranded anti-parallel (3-sheet flanked by a-helices on both sides. One long helix, termed... 

SCOP, CATH, and DDD agree on most of their classifications, despite differences in the classification methods they have implemented, and in the rules of protein structure and taxonomy they are based on. Hadley and Jones were the first to publish a detailed comparison of the fold classifications produced by SCOP, CATH, and FSSP. They showed that the three classification systems tend to agree in most cases, and that the discrepancies and inconsistencies are accounted for by a small number of problems. Among these, the domain assignment plays a crucial role. As mentioned, the separation of proteins into domains is a difficult and often subjective process. Many... 

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