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Guaranteed Discrete Energy Optimization on Large Protein Design Problems

Abstract : 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 10(234). 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.
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https://hal.inrae.fr/hal-02637306
Contributor : Migration Prodinra <>
Submitted on : Wednesday, May 27, 2020 - 10:42:58 PM
Last modification on : Thursday, August 5, 2021 - 3:54:36 AM

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David Simoncini, David Allouche, Simon de Givry, Céline Delmas, Sophie Barbe, et al.. Guaranteed Discrete Energy Optimization on Large Protein Design Problems. Journal of Chemical Theory and Computation, American Chemical Society, 2015, 11 (12), pp.5980 - 5989. ⟨10.1021/acs.jctc.5b00594⟩. ⟨hal-02637306⟩

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