Parallel Tree Search-based Protein Conformation Analysis System
Implemented on a Massively Parallel Computer
Makoto Ando, Yutaka Akiyama, Kentaro Onizuka and Tamotsu Noguchi
In this paper, we report on the design and the implementation of the
Parallel Tree Search-based Protein Conformation Analysis System. In
our protein conformation analysis model, we assume that the atoms in a
protein are hard spheres with certain radii, and the single covalent
bonds are turnable axes. The conformational isomers are generated by
varying the torsion angles of all the turnable axes, and each
generated conformational isomer is checked for validity. Distance
constraints and angle constraints greatly reduce the size of the
search space. Using these constraints, our system succeeded in
analyzing the conformations of an opioid peptide, one of the important
peptides in drug design. The parallel version of our program showed
good speedups over the sequential version (192-fold speedup using 256
PUs).