ESCAPE 2.0: parallel exhaustive conformational search system of peptides with conformational libraries as building blocks

摘要

We report on the design and the implementation of ESCAPE 2.0, the parallel exhaustive conformational search system for 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. 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 one to analyze compounds that have rings of variable shapes. For analyses with distance constraints on the relative positions of atoms, ESCAPE 2.0 successfully reduced the size of the search tree, and analyzed a peptide of 5 amino acid length within several seconds. For analyses without distance constraints, a parallel version of ESCAPE 2.0 showed good speedups over the sequential version.