A method to detect nonproline cis peptide bonds in proteins

Based on the geometrical parameters around seventeen incorrectly assigned t rans conformations of peptide bonds in protein structures and their correct cis counterparts, we have devised an algorithm that is capable of detectin g these sites. The algorithm was optimized to reliably find all of the the seventeen rest cases. It carl be used to quickly scan an atomic coordinate file or the complete Brookhaven Protein Data Base for more likely candidate s for non-Pro cis peptide bonds. Also, it can be of help to guide the cryst allographer in intermediate stages of structure determination towards suspe ct areas. (C) 1999 John Wiley & Sons, Inc.