{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,9]],"date-time":"2026-07-09T00:37:58Z","timestamp":1783557478642,"version":"3.55.0"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":3426,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Summary: 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\u2013function relationships and the design of CYPs with improved biochemical properties.<\/jats:p><jats:p>Abbreviations: Cytochrome P450 Engineering Database, CYPED; cytochrome P450 monooxygenase, CYP; Hidden Markov Model, HMM.<\/jats:p><jats:p>Availability: \u00a0www.cyped.uni-stuttgart.de<\/jats:p><jats:p>Contact: \u00a0Juergen.Pleiss@itb.uni-stuttgart.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm268","type":"journal-article","created":{"date-parts":[[2007,5,18]],"date-time":"2007-05-18T16:49:30Z","timestamp":1179506970000},"page":"2015-2017","source":"Crossref","is-referenced-by-count":105,"title":["The Cytochrome P450 Engineering Database: a navigation and prediction tool for the cytochrome P450 protein family"],"prefix":"10.1093","volume":"23","author":[{"given":"Markus","family":"Fischer","sequence":"first","affiliation":[{"name":"1 Department 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"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Knoll","sequence":"additional","affiliation":[{"name":"1 Department 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"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Demet","family":"Sirim","sequence":"additional","affiliation":[{"name":"1 Department 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"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Florian","family":"Wagner","sequence":"additional","affiliation":[{"name":"1 Department 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"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sonja","family":"Funke","sequence":"additional","affiliation":[{"name":"1 Department 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"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juergen","family":"Pleiss","sequence":"additional","affiliation":[{"name":"1 Department 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"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2007,5,17]]},"reference":[{"key":"2023041105314337500_","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2023041105314337500_","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1093\/nar\/gkg057","article-title":"GenBank","volume":"31","author":"Benson","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023041105314337500_","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1093\/nar\/gkg015","article-title":"The Lipase Engineering Database: a navigation and analysis tool for protein families","volume":"31","author":"Fischer","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023041105314337500_","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1186\/1471-2105-7-495","article-title":"DWARF \u2013 a data warehouse system for analyzing protein families","volume":"7","author":"Fischer","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023041105314337500_","doi-asserted-by":"crossref","first-page":"2577","DOI":"10.1002\/bip.360221211","article-title":"Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features","volume":"22","author":"Kabsch","year":"1983","journal-title":"Biopolymers"},{"key":"2023041105314337500_","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1016\/j.taap.2003.11.030","article-title":"Structural basis for the role in protein folding of conserved proline-rich regions in cytochromes P450","volume":"199","author":"Kemper","year":"2004","journal-title":"Toxicol Appl. 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