SUPERFAMILY, protein database

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. 

For those interested in statistics, in September 1998, there were 7657 structures deposited in the Brookhaven Protein Database (http //www.pdb.bnl.gov). These are analyzed on the scop database (http //scop.mrc-lmb.cam.ac.uk) into 435 folds, 640 superfamilies, 948 families, and 14 903 domains. There are probably about 1000 different superfamilies.35... 

The protein sequence database is also a text-numeric database with bibliographic links. It is the largest public domain protein sequence database. The current PIR-PSD release 75.04 (March, 2003) contains more than 280 000 entries of partial or complete protein sequences with information on functionalities of the protein, taxonomy (description of the biological source of the protein), sequence properties, experimental analyses, and bibliographic references. Queries can be started as a text-based search or a sequence similarity search. PIR-PSD contains annotated protein sequences with a superfamily/family classification. 

It is important to emphasize that this lattice database is highly idealized compared to real databases. Unlike the lattice database, real databases cannot be treated as thermodynamic ensembles of protein-ligand complexes equilibrated at room temperature [33,34]. Two of the more straightforward reasons are mentioned here. First, real databases are inherently biased toward strong binders (K < 10 pM), because weak binders are difficult to crystallize and of lesser interest. Second, as mentioned above, real databases are not composed of a representative selection of proteins and ligands, and their compositions are biased toward peptide and peptidomimetic inhibitors and certain protein superfamilies. In contrast, because only one protein and four ligand types are used, the lattice database should have representative ligand compositions. 

Selected entries from Methods in Enzymology [vol, page(s)] Databases and Resources Information services of European Bioinformatics Institute, 266, 3 TDB new databases for biological discovery, 266, 27 PIR-international protein sequence database, 266, 41 superfamily classification in PIR-international protein sequence database, 266, 59 gene classification artificial neural system, 266, 71 blocks database and its applications, 266, 88 indexing and using sequence databases, 266, 105 SRS information retrieval system for molecular biology data banks, 266, 114. 

Blue copper proteins have been purified and biochemically characterized from Archaea, Bacteria, and Eukarya. Such ubiquitous distribution suggests an important ancient role. A survey of sequence databases reveals genes encoding blue copper proteins that display characteristics often quite different from those of well-studied canonical (traditional) blue copper proteins. For example, there are modular proteins where the domains that bind type 1 copper are fused with structurally distinct and evolutionarily unrelated sequence motifs (Figure 1). While these additional domains do not usually contribute directly to the ftmction of a blue copper protein, they do so indirectly by facilitating protein translocation to a specific cellular compartment. Together, these blue copper proteins can be combined into a large superfamily which can be subdivided into three classes as described below. 

Hotelier T, Renault L, Cousin X, Negre V, Marchot P, Chaton-net A. ESTHER, the database of the alpha/beta-hydrolase fold superfamily of proteins. Nucleic Acids Res. 2004 32 D145-147. 

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