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

Kirshner, Daniel A.
Nilmeier, Jerome P.
Lightstone, Felice C.

Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA

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Received 19 February 2013; revised 17 April 2013; accepted 22 April 2013

Nucleic Acids Research 41:p W256-W265, July 1, 2013. | DOI: 10.1093/nar/gkt403

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 athttp://catsid.llnl.gov.