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A Variable Neighbourhood Descent Heuristic for Conformational Search Using a Quantum Annealer.

ABSTRACT: Discovering the low-energy conformations of a molecule is of great interest to computational chemists, with applications in in silico materials design and drug discovery. In this paper, we propose a variable neighbourhood search heuristic for the conformational search problem. Using the structure of a molecule, neighbourhoods are chosen to allow for the efficient use of a binary quadratic optimizer for conformational search. The method is flexible with respect to the choice of molecular force field and the number of discretization levels in the search space, and can be further generalized to take advantage of higher-order binary polynomial optimizers. It is well-suited for the use of devices such as quantum annealers. After carefully defining neighbourhoods, the method easily adapts to the size and topology of these devices, allowing for seamless scaling alongside their future improvements.

SUBMITTER: Marchand DJJ

PROVIDER: S-EPMC6757033 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature

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A Variable Neighbourhood Descent Heuristic for Conformational Search Using a Quantum Annealer.

Marchand D J J DJJ Noori M M Roberts A A Rosenberg G G Woods B B Yildiz U U Coons M M Devore D D Margl P P

Scientific reports 20190923 1

Discovering the low-energy conformations of a molecule is of great interest to computational chemists, with applications in in silico materials design and drug discovery. In this paper, we propose a variable neighbourhood search heuristic for the conformational search problem. Using the structure of a molecule, neighbourhoods are chosen to allow for the efficient use of a binary quadratic optimizer for conformational search. The method is flexible with respect to the choice of molecular force fi ...[more]

PMID: 31548549

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