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Bioinformatics Advance Access published online on May 17, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm268
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© 2007 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.

The Cytochrome P450 Engineering Database: A Navigation and Prediction Tool for the Cytochrome P450 Protein Family

Markus Fischer 1, Michael Knoll 2, Demet Sirim 2, Florian Wagner 2, Sonja Funke 2 and Jürgen Pleiss 2,*

1Dept of Biochemistry & Molecular Biophysics, Columbia University, 1130 St. Nicholas Ave, New York, NY 10032, USA and 2Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany

*To whom correspondence should be addressed. Jürgen Pleiss, E-mail: Juergen.Pleiss{at}itb.uni-stuttgart.de


  Abstract

Motivation: The Cytochrome P450 Engineering Database (CYPED) has been designed to serve as a tool for a comprehensive and systematic comparison of protein sequences and structures within the vast and diverse family of cytochrome P450 monooxygenases (CYPs). The CYPED currently integrates sequence and structure data of 3911 and 25 proteins, respectively. Proteins are grouped into homologous families and superfamilies according to Nelson's classification. Nonclassified CYP sequences are assigned by similarity. Functionally relevant residues are annotated. The web accessible version contains multisequence alignments, phylogenetic trees and HMM profiles. The CYPED is regularly updated and supplies all data for download. Thus, it provides a valuable data source for phylogenetic analysis, investigation of sequence-function relationships, and the design of CYPs with improved biochemical properties.

Abbreviations: Cytochrome P450 Engineering Database, CYPED; cytochrome P450 monooxygenase, CYP; Hidden Markov Model, HMM.

Availability: www.cyped.uni-stuttgart.de

Associate Editor: Dr. Alex Bateman

Received on March 20, 2007; revised on May 7, 2007; accepted on May 10, 2007

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