Structure databases classification

SCOP Structural Classification of Proteins. Hierarchical protein structure database... 

Selected entries from Methods in Enzymology [vol, page(s)] General Protein kinase classification, 200, 3 protein kinase catalytic domain sequence database identification of conserved features of primary structure and classification of family members,... 

In this section, enzymes in the EC 2.4. class are presented that catalyze valuable and interesting reactions in the field of polymer chemistry. The Enzyme Commission (EC) classification scheme organizes enzymes according to their biochemical function in living systems. Enzymes can, however, also catalyze the reverse reaction, which is very often used in biocatalytic synthesis. Therefore, newer classification systems were developed based on the three-dimensional structure and function of the enzyme, the property of the enzyme, the biotransformation the enzyme catalyzes etc. [88-93]. The Carbohydrate-Active enZYmes Database (CAZy), which is currently the best database/classification system for carbohydrate-active enzymes uses an amino-acid-sequence-based classification and would classify some of the enzymes presented in the following as hydrolases rather than transferases (e.g. branching enzyme, sucrases, and amylomaltase) [91]. Nevertheless, we present these enzymes here because they are transferases according to the EC classification. 

Molecular databases and the associated data banks require the development of a conceptual structure for the information stored about the molecules, descriptive language representing the data, and methods for analysis enabling molecular modeling, similarity searches, classification, visualization, or other uses of the database.320 Currendy, the Protein Data Bank (PDB http 7www.rcsb.org/pdb/) is one of the best known examples of a molecular database. The PDB is a worldwide archive of three-dimensional structural data of biological macromolecules.321 The PDB is a common accentor to many structural databases.322 The success of... 

Classification of Chemical Structure Databases Using a Highly Parallel Array Processor. 

At present there are >100 protein kinase-inhibitor structures in publidy available structural databases which span 28 kinases and a variety of inhibitor structural classes. Based upon an analysis of these data a classification of ATP binding regions has been proposed by Traxler and Furet [59] and Bower (personal communication from Michael J. Bower, December 1999). In the subsequent discussion a slightly modified version of this classification will be used to organize the trends seen across kinases and inhibitor dasses (see Fig. 2.2). In the Traxler model, five sites were proposed of which three (adenine, sugar and phosphate-binding sites) can be directly related to ATP and two additional lipophilic sites which lay outside of the region occupied by ATP. In the Bower model, an additional polar site on the surface of the protein was proposed. 

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/). 

In addition to the above mentioned databases that try to cover the entire world of enzymes, there are a number of more topical databases focusing on particular enzyme families. The MEROPS database, maintained at the Babraham Institute in Cambridge, provides a catalog and a structure-based classification scheme for all proteolytic enzymes 58. In addition to the classification, the database also provides a digest of published information on the peptidases as well as dadograms and multiple sequence alignments of the peptidase families. 

A comprehensive classification system for lipids with broad support in the lipid research community can be found at the Lipid Maps Structure Database (www. Upidmaps.org). The Lipid Maps Structure Database currently catalogs over 10,000 structures. 

Secondary protein structural databases (structural motifs and classifications) ... 

The most difficult application of protein structure comparison comes in classifying known protein structures into different clusters corresponding to fold families. The role of such classifications is to organize structure databases such as the PDB, in hopes of detecting similarities at the structure level that... 

E.M. Rasmussen, G. M. Downs, andP. Willett,/. CompM. Chem., 9,378 (1988). Automatic Classification of Chemical Structure Databases Using a Highly Parallel Arrray Processor. 

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