D588–D592 Nucleic Acids Research, 2009, Vol. 37, Database issue doi:10.1093/nar/gkn820 Published online 4 November 2008 BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009 Antje Chang, Maurice Scheer, Andreas Grote, Ida Schomburg and Dietmar Schomburg* Technical University Braunschweig, Institute for Bioinformatics and Biochemistry, Langer Kamp 19 B, 38106 Braunschweig, Germany Received September 12, 2008; Revised and Accepted October 13, 2008 ABSTRACT The BRENDA (BRaunschweig ENzyme DAtabase) (http://www.brenda-enzymes.org) represents the largest freely available information system contain- ing a huge amount of biochemical and molecular information on all classified enzymes as well as software tools for querying the database and calcu- lating molecular properties. The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data. The data in BRENDA are manually curated from more than 79 000 primary literature references. Each entry is clearly linked to a literature reference, the origin organism and, where available, to the protein sequence of the enzyme protein. A new search option provides the access to protein- specific data. FRENDA (Full Reference ENzyme DAta) and AMENDA (Automatic Mining of ENzyme DAta) are additional databases created by continu- ously improved text-mining procedures. These databases ought to provide a complete survey on enzyme data of the literature collection of PubMed. The web service via a SOAP (Simple Object Access Protocol) interface for access to the BRENDA data has been further enhanced. INTRODUCTION The development of the BRENDA (BRaunschweig ENzyme DAtabase) enzyme information system was started in 1987 at the former German National Research Centre for Biotechnology (now: Helmholtz Centre for Infection Research) in Braunschweig. Originally published as a series of books (1) it was curated and continuously improved at the University of Cologne from 1996 to 2007. In this period it was transformed into a publicly avail- able database (2). Since 2007, BRENDA is maintained and curated at the Technische Universita¨ t Braunschweig, Institute of Bioinformatics & Systems Biology. Since the last publication (3), major new developments and improve- ments have been integrated. A new search option oﬀers direct querying of protein-speciﬁc data. AMENDA (Auto- matic Mining of ENzyme DAta) and FRENDA (Full Reference ENzyme DAta) have been developed as addi- tional databases based on text-mining procedures and are completely reprogrammed to improve the quality and to reduce false positive entries. BRENDA provides an intuitive search engine with a number of widely diﬀerent possibilities to access the data, stored in a relational database system. The Quick Search performs a direct search in one of the 53 data ﬁelds; the Advanced Search allows a combinatorial search of up to 20 search categories for text or numerical data ﬁelds. The Fullltext Search performs a search in all sections of the database including comments. Further- more the Substructure Search allows to explore enzyme– ligand interactions. Enzyme catalyzed reactions can be viewed as graphical representations. The Ontology Explorer allows to simultanously search in all biochemically relevant ontologies, among them BTO (BrendaTissueOntology), which is constantly curated by the BRENDA team and contains now approximately 3400 terms on tissues, organs and cell types. The Genome Explorer connects enzymes to genome sequences. The locations of classiﬁed enzymes are displayed in their geno- mic context. The Taxonomy Tree Explorer provides a search for enzymes or organisms in the taxonomic tree. The EC Explorer can be used to browse or search the hierarchical tree of enzymes. The Sequence Search is *To whom correspondence should be addressed. Tel: +49 221 470 6440; Fax: +49 221 470 5092; Email: d.schomburg@tu-bs.de 2008 The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.