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Entropy 2016, 18(10), 365; doi:10.3390/e18100365

Boltzmann Sampling by Degenerate Optical Parametric Oscillator Network for Structure-Based Virtual Screening

1
Department of Electrical Engineering and Information Systems, The University of Tokyo, Tokyo 113-8654, Japan
2
RIKEN Innovation Center, Saitama 351-0198, Japan
3
The KAITEKI Institute, Inc.,Tokyo 100-8251, Japan
4
National Institute of Informatics, Tokyo 101-8403, Japan
5
ImPACT Program, The Japan Science and Technology Agency, Tokyo 102-0076, Japan
6
Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan
*
Author to whom correspondence should be addressed.
Academic Editor: Jay Lawrence
Received: 3 September 2016 / Revised: 10 October 2016 / Accepted: 11 October 2016 / Published: 13 October 2016
(This article belongs to the Collection Quantum Information)
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Abstract

A structure-based lead optimization procedure is an essential step to finding appropriate ligand molecules binding to a target protein structure in order to identify drug candidates. This procedure takes a known structure of a protein-ligand complex as input, and structurally similar compounds with the query ligand are designed in consideration with all possible combinations of atomic species. This task is, however, computationally hard since such combinatorial optimization problems belong to the non-deterministic nonpolynomial-time hard (NP-hard) class. In this paper, we propose the structure-based lead generation and optimization procedures by a degenerate optical parametric oscillator (DOPO) network. Results of numerical simulation demonstrate that the DOPO network efficiently identifies a set of appropriate ligand molecules according to the Boltzmann sampling law. View Full-Text
Keywords: degenerate optical parametric oscillator (DOPO); structure-based drug design; coherent Ising machine; combinatorial optimization problem degenerate optical parametric oscillator (DOPO); structure-based drug design; coherent Ising machine; combinatorial optimization problem
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Sakaguchi, H.; Ogata, K.; Isomura, T.; Utsunomiya, S.; Yamamoto, Y.; Aihara, K. Boltzmann Sampling by Degenerate Optical Parametric Oscillator Network for Structure-Based Virtual Screening. Entropy 2016, 18, 365.

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