SCOP, CATH, and DDD

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 

Despite these discrepancies, Hadley and Jones recognized the merits of all three classifications and concluded that no one method is distincdy superior to another. They characterize SCOP as a valuable resource for detailed evolutionary information, CATH as a source of geometric information, and FSSP as a raw source of information, which is continually updated. 

The three major protein structure classifications are SCOP, CATH, and DDD. SCOP is derived manually and is recognized as a valuable resource of detailed evolutionary information. CATH provides useful geometric information. It also introduces the concept of architecture, which reveals broad features of the protein structure space. CATH relies on partial automation and as such is subject to inaccuracies introduced by fixed thresholds. The DDD is a fully automatic classification continually updated. It is not as popular as SCOP and CATH, probably because its automatic levels are not as intuitive and require more input from the users to be interpreted. 

Protein structure classifications need to be linked with the other genome databases under constructions. Currently, SCOP, CATH, and DDD are valuable resources used mostly for benchmarking of methods and for structural studies. Their impact on biology will be far greater when they are integrated with sequence and function information to present a cohesive picture of the different protein spaces. 

Support from the National Science Foundation (Grant CCR-00-86013) and the National Institute of Health (GM 63817) is acknowlet ed. 

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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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