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Computational Protein Design Using AND/OR Branch-and-Bound Search

  • Yichao Zhou
  • Yuexin Wu
  • Jianyang ZengEmail author
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9029)

Abstract

The computation of the global minimum energy conformation (GMEC) is an important and challenging topic in structure-based computational protein design. In this paper, we propose a new protein design algorithm based on the AND/OR branch-and-bound (AOBB) search, which is a variant of the traditional branch-and-bound search algorithm, to solve this combinatorial optimization problem. By integrating with a powerful heuristic function, AOBB is able to fully exploit the graph structure of the underlying residue interaction network of a backbone template to significantly accelerate the design process. Tests on real protein data show that our new protein design algorithm is able to solve many problems that were previously unsolvable by the traditional exact search algorithms, and for the problems that can be solved with traditional provable algorithms, our new method can provide a large speedup by several orders of magnitude while still guaranteeing to find the global minimum energy conformation (GMEC) solution.

Keywords

Protein design AND/OR branch-and-bound Global minimum energy conformation Residue interaction network Mini-bucket heuristic 

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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  1. 1.Institute for Interdisciplinary Information SciencesTsinghua UniversityBeijingPeople’s Republic of China
  2. 2.MOE Key Laboratory of BioinformaticsTsinghua UniversityBeijingPeople’s Republic of China

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