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Catalytic site identification--a web server to identify catalytic site structural matches throughout PDB.

ABSTRACT: The catalytic site identification web server provides the innovative capability to find structural matches to a user-specified catalytic site among all Protein Data Bank proteins rapidly (in less than a minute). The server also can examine a user-specified protein structure or model to identify structural matches to a library of catalytic sites. Finally, the server provides a database of pre-calculated matches between all Protein Data Bank proteins and the library of catalytic sites. The database has been used to derive a set of hypothesized novel enzymatic function annotations. In all cases, matches and putative binding sites (protein structure and surfaces) can be visualized interactively online. The website can be accessed at http://catsid.llnl.gov.

SUBMITTER: Kirshner DA

PROVIDER: S-EPMC3692059 | biostudies-literature | 2013 Jul

REPOSITORIES: biostudies-literature

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Catalytic site identification--a web server to identify catalytic site structural matches throughout PDB.

Kirshner Daniel A DA Nilmeier Jerome P JP Lightstone Felice C FC

Nucleic acids research 20130516 Web Server issue

The catalytic site identification web server provides the innovative capability to find structural matches to a user-specified catalytic site among all Protein Data Bank proteins rapidly (in less than a minute). The server also can examine a user-specified protein structure or model to identify structural matches to a library of catalytic sites. Finally, the server provides a database of pre-calculated matches between all Protein Data Bank proteins and the library of catalytic sites. The databas ...[more]

PMID: 23680785

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