Determining Protein Structure using the Distance Geometry Program APA

APA is a computer program, written in C, designed to determine the three-dimensional structure of proteins using distance geometry. We present the sampling and convergence properties of APA, as tested on bovine pancreatic trypsin inhibitor (BPTI). The results con®rm the program's earlier success with poly-L-alanine, albeit with some complications. The correct overall orientation of the BPTI conformation is achieved at an early stage in the algorithm. The correct orientations of the a-carbons are obtained by local re ̄ections, 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 Havel's DG-II distance geometry program, the sampling and convergence properties were tested on Havel's 10 data sets. These simulated data sets were generated from the BPTI crystal and kindly provided by Tim Havel. # 1999 Elsevier Science Ltd. All rights reserved.