ESCAPE: Parallel Tree Search System for Conformational Analysis of Peptides
Makoto Ando, Yutaka Akiyama, Kentaro Onizuka and Tamotsu Noguchi
In this paper, we report on the design and the implementation of ESCAPE, the Parallel Tree Search System for Conformational Analysis of Peptides.
We employed an exhaustive search method for conformational searches, and this gives our system an ability to analyze conformations even if the whole physicochemical environment of the target peptide segment is unknown.
We have implemented the system, and successfully analyzed the conformations of twenty amino acid residues individually.
We also analyzed the conformations of a peptide segment which is important for drug design.
The parallel version of ESCAPE showed good speedups over the sequential version (194-fold speedup using 256 PEs).