ESCAPE 2.0: Parallel Exhaustive Conformational Search
System of Peptides with Conformational Libraries as Building Blocks
Makoto Ando, Yutaka Akiyama and Hideo Matsuda
In this paper, we report on the design and the implementation of
ESCAPE 2.0, the parallel exhaustive conformational search system of
peptides. We employed an exhaustive search method for conformational
searches, so that ESCAPE 2.0 does not overlook any important
conformations that may be overlooked by other systems based on
probabilistic approaches. Although the previous version of ESCAPE can
analyze short peptide segments, we added new functions in order to
analyze larger problems: Tree Search Rotamer Libraries reduce the size
of the search space, and the Variable Ring Conformation Libraries
enable to analyze the compounds that have rings of variable
shapes. For the analyses with distance constraints on relative
positions of atoms, ESCAPE 2.0 successfully reduce the size of search
tree, and analyze the peptide of 5 amino acids length within several
seconds. For the analyses without distance constraints, parallel
version of ESCAPE 2.0 showed good speedups over the sequential
version.
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