Computational Protein Design Using AND/OR Branch-and-Bound Search
نویسندگان
چکیده
منابع مشابه
Computational Protein Design Using AND/OR Branch-and-Bound Search
The computation of the global minimum energy conformation (GMEC) is an important and challenging topic in structure-based computational protein design. In this article, we propose a new protein design algorithm based on the AND/OR branch-and-bound (AOBB) search, a variant of the traditional branch-and-bound search algorithm, to solve this combinatorial optimization problem. By integrating with ...
متن کاملAppendix of “Computational Protein Design Using AND/OR Branch and Bound Search”
Suppose we try to find the global minimum value of the energy function E(r), in which r ∈ R and R is the conformational space of the rotamers. The BnB algorithm executes two steps recursively. The first step is called branching, in which we split the conformational space R into two or more smaller spaces, i.e., R1, R2, . . . , Rm, where R1 ∪ R2 ∪ · · · ∪ Rm = R. If we are able to find r̂i = argm...
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A branch-and-bound approach to solving influence diagrams has been previously proposed in the literature, but appears to have never been implemented and evaluated – apparently due to the difficulties of computing effective bounds for the branch-and-bound search. In this paper, we describe how to efficiently compute effective bounds, and we develop a practical implementation of depth-first branc...
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ژورنال
عنوان ژورنال: Journal of Computational Biology
سال: 2016
ISSN: 1066-5277,1557-8666
DOI: 10.1089/cmb.2015.0212