The Cytochrome P450 Engineering Database: a navigation and prediction tool for the cytochrome P450 protein family.
CONCLUSIONS
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.


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


BACKGROUND
www.cyped.uni-stuttgart.de
Fischer
Markus
M
Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA.
Knoll
Michael
M
Sirim
Demet
D
Wagner
Florian
F
Funke
Sonja
S
Pleiss
Juergen
J
D000465:Algorithms; D003196:Computer Graphics; D003198:Computer Simulation; D003577:Cytochrome P-450 Enzyme System / Q000737:chemistry* / Q000145:classification / Q000235:genetics*; D003628:Database Management Systems; D030562:Databases, Protein; D016247:Information Storage and Retrieval / Q000379:methods; D008956:Models, Chemical; D008958:Models, Molecular; D015202:Protein Engineering / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods; D012984:Software; D014584:User-Computer Interface
D003577:Cytochrome P-450 Enzyme System