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Bioinformatics Advance Access originally published online on October 27, 2004
Bioinformatics 2005 21(5):685-686; doi:10.1093/bioinformatics/bti089
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Published by Oxford University Press 2004.

COPS—Cis/trans peptide bond conformation prediction of amino acids on the basis of secondary structure information

Doreen Pahlke 1, Dietmar Leitner 1,2, Urs Wiedemann 1 and Dirk Labudde 1,2,*

1 Forschungsinstitut für Molekulare Pharmakologie Robert-Rössle-Str. 10, 13125 Berlin, Germany
2 The Berlin Structure Factory Project Heubnerweg 6, 14059 Berlin, Germany

*To whom correspondence should be addressed.

Summary: COPS predicts for all 20 naturally occurring amino acids whether the peptide bond in a protein is in cis or trans conformation. The algorithm is based only on secondary structure information of amino acid triplets without considering the amino acid sequence information. Conformation parameters are derived from solved 3D structures deposited in the PDB and led to propensities based on modified Chou–Fasman parameters. COPS analyses amino acid triplets taking only their respective secondary structure into consideration and upon application of a set of rules utilizing the conformation parameters, the N-terminal peptide bond conformation of the middle residue is predicted. COPS was tested on a random selection of protein datasets.

Availability: The COPS program and further information are freely available from the FMP website at http://www.fmp-berlin.de/nmr/cops

Contact: labudde{at}fmp-berlin.de


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