ESTHER, the database of the α/β-hydrolase fold superfamily of proteins: tools to explore diversity of functions

Nucleic Acids Res. 2013 Jan;41(Database issue):D423-9. doi: 10.1093/nar/gks1154. Epub 2012 Nov 27.

Abstract

The ESTHER database, which is freely available via a web server (http://bioweb.ensam.inra.fr/esther) and is widely used, is dedicated to proteins with an α/β-hydrolase fold, and it currently contains >30 000 manually curated proteins. Herein, we report those substantial changes towards improvement that we have made to improve ESTHER during the past 8 years since our 2004 update. In particular, we generated 87 new families and increased the coverage of the UniProt Knowledgebase (UniProtKB). We also renewed the ESTHER website and added new visualization tools, such as the Overall Table and the Family Tree. We also address two topics of particular interest to the ESTHER users. First, we explain how the different enzyme classifications (bacterial lipases, peptidases, carboxylesterases) used by different communities of users are combined in ESTHER. Second, we discuss how variations of core architecture or in predicted active site residues result in a more precise clustering of families, and whether this strategy provides trustable hints to identify enzyme-like proteins with no catalytic activity.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteria / enzymology
  • Catalytic Domain
  • Databases, Protein*
  • Esterases / chemistry
  • Esterases / classification
  • Hydrolases / chemistry*
  • Hydrolases / classification*
  • Internet
  • Lipase / chemistry
  • Lipase / classification
  • Protein Folding
  • Serine Endopeptidases / chemistry
  • Serine Endopeptidases / classification
  • Software
  • Thiolester Hydrolases / chemistry
  • Thiolester Hydrolases / classification

Substances

  • Hydrolases
  • Esterases
  • Lipase
  • Thiolester Hydrolases
  • Serine Endopeptidases