A Hierarchical Approach to Parallel Tree Search-based
Protein Conformational Analysis
Makoto Ando, Yutaka Akiyama and Hideo Matsuda
In this paper, we report on a new model for the protein conformational
analysis by parallel tree search, which is based on our previous
works. In the new model, the original problem can be divided into
several subproblems, and the search tree of the original problem can
be build using the results of the subproblems. Because the search
spaces obtained from the results of the subproblems do not contain any
branches for invalid conformations, we can reduce the size of the
search space of the original problem. We show the effects of the new
model by analyzing the conformations of amino acids and the tyrosine
corner, which we can find in real proteins.