Parallel Tree Search-based Protein Conformation Analysis System
Makoto Ando, Yutaka Akiyama, Kentaro Onizuka, Tamotsu Noguchi
We have developed the Parallel Protein Conformation Analysis System,
based on our implementation techniques used in parallel tree search
programs. We employed an exhaustive search method for conformation
search, rotating all the rotatable bonds by specified grain. We have
implemented the system, and succeeded in analyzing the conformations
of 20 amino acids individually. The parallel version of our program
showed good speedups over the sequential version. We also succeeded in
overlapping task management operations onto tree search operations by
assigning them to multiple processes. We are aiming at analyzing the
conformations of several amino acids that is useful in drug design.