Guaranteed discrete energy optimization on large protein design problems

D Simoncini, D Allouche, S De Givry… - Journal of chemical …, 2015 - ACS Publications
Journal of chemical theory and computation, 2015ACS Publications
In Computational Protein Design (CPD), assuming a rigid backbone and amino-acid rotamer
library, the problem of finding a sequence with an optimal conformation is NP-hard. In this
paper, using Dunbrack's rotamer library and Talaris2014 decomposable energy function, we
use an exact deterministic method combining branch and bound, arc consistency, and tree-
decomposition to provenly identify the global minimum energy sequence-conformation on
full-redesign problems, defining search spaces of size up to 10234. This is achieved on a …
In Computational Protein Design (CPD), assuming a rigid backbone and amino-acid rotamer library, the problem of finding a sequence with an optimal conformation is NP-hard. In this paper, using Dunbrack’s rotamer library and Talaris2014 decomposable energy function, we use an exact deterministic method combining branch and bound, arc consistency, and tree-decomposition to provenly identify the global minimum energy sequence-conformation on full-redesign problems, defining search spaces of size up to 10234. This is achieved on a single core of a standard computing server, requiring a maximum of 66GB RAM. A variant of the algorithm is able to exhaustively enumerate all sequence-conformations within an energy threshold of the optimum. These proven optimal solutions are then used to evaluate the frequencies and amplitudes, in energy and sequence, at which an existing CPD-dedicated simulated annealing implementation may miss the optimum on these full redesign problems. The probability of finding an optimum drops close to 0 very quickly. In the worst case, despite 1,000 repeats, the annealing algorithm remained more than 1 Rosetta unit away from the optimum, leading to design sequences that could differ from the optimal sequence by more than 30% of their amino acids.
ACS Publications
以上显示的是最相近的搜索结果。 查看全部搜索结果