ESCAPE 2.0: Prallel Exhaustive Conformational Search System of Peptides with Conformational Libraries as Building Blocks

摘要

In this paper, we report on the design and the implemenptation of ESCAPE2.0, the parallel exhaustive conforma-tional search system of peptides. We employed an exhaus-tive search method for conformational searches. so that ES-CAPE 2.0 does not overlook any important conformations that may be overlooked by other systems. Although the previous version of ESCAPE can analyze shout peptide seg-ments, 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 Li-braries 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 re-duce the size of search tree, and analyze the peptide of 5amino acids length within several seconds. For the analyses without distance constraintd, parallel version of ESCAPE 2.0 showed good speedups over the sequential version.