Determining protein structure using the distance geometry program APA

APA is a computer program, written in C, designed to determine the three-di mensional structure of proteins using distance geometry. We present the sam pling and convergence properties of APA, as tested on bovine pancreatic try psin inhibitor (BPTI). The results confirm the program's earlier success wi th poly-L-alanine, albeit with some complications. The correct overall orie ntation of the BPTI conformation is achieved at an early stage in the algor ithm. The correct orientations of the alpha-carbons are obtained by local r eflections, instead of a penalty term, resulting in a smoother convergence. Finally, a process of choosing dissimilarities from two reduced data sets resulted in almost all structures converging. In order to compare with Have l's DG-II distance geometry program, the sampling and convergence propertie s were tested on Havel's 10 data sets. These simulated data sets were gener ated from the BPTI crystal and kindly provided by Tim Havel. (C) 1999 Elsev ier Science Ltd. All rights reserved.