title: The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes.
abstract: Understanding which are the catalytic residues in an enzyme and what function they perform is crucial to many biology studies, particularly those leading to new therapeutics and enzyme design. The original version of the Catalytic Site Atlas (CSA) (http://www.ebi.ac.uk/thornton-srv/databases/CSA) published in 2004, which catalogs the residues involved in enzyme catalysis in experimentally determined protein structures, had only 177 curated entries and employed a simplistic approach to expanding these annotations to homologous enzyme structures. Here we present a new version of the CSA (CSA 2.0), which greatly expands the number of both curated (968) and automatically annotated catalytic sites in enzyme structures, utilizing a new method for annotation transfer. The curated entries are used, along with the variation in residue type from the sequence comparison, to generate 3D templates of the catalytic sites, which in turn can be used to find catalytic sites in new structures. To ease the transfer of CSA annotations to other resources a new ontology has been developed: the Enzyme Mechanism Ontology, which has permitted the transfer of annotations to Mechanism, Annotation and Classification in Enzymes (MACiE) and UniProt Knowledge Base (UniProtKB) resources. The CSA database schema has been re-designed and both the CSA data and search capabilities are presented in a new modern web interface.
authors: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and Department of Biochemistry and Molecular Genetics, University of Virginia, 1300 Jefferson Park Ave., Charlottesville, VA 22908, USA.
authors: Nicholas
authors: N
authors: Furnham
authors: Gemma L
authors: GL
authors: Holliday
authors: Tjaart A P
authors: TA
authors: de Beer
authors: Julius O B
authors: JO
authors: Jacobsen
authors: William R
authors: WR
authors: Pearson
authors: Janet M
authors: JM
authors: Thornton
mesh_terms: D064229:Biological Ontologies; D020134:Catalytic Domain; D030562:Databases, Protein; D004798:Enzymes / Q000737:chemistry*; D020407:Internet; D020539:Sequence Analysis, Protein
chemical_list: D004798:Enzymes