ESCAPE: Parallel Tree Search System for Conformational Analysis of Peptides
Makoto Ando, Yutaka Akiyama, Kentaro Onizuka and Tamotsu Noguchi
In order to analyze the conformations of short peptides that are useful in drug design, we developed 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.
ESCAPE does not use any statistical rotamer information, and it can analyze peptide conformations which contain exceptional residues (other than twenty common amino acids).
ESCAPE successfully analyzed the conformations of twenty amino acid residues individually.
It also analyzed the conformations of a peptide segment of an opioid peptide, Tyr-Gly-Gly-Phe, considering all the hydrogen atoms in the segment for accuracy.
The parallel version of ESCAPE showed excellent speedups over the sequential version (194-fold speedup using 256 processors).
Real World Computing Partnership