COPS--cis/trans peptide bond conformation prediction of amino acids on the basis of secondary structure information.

Abstract

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