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

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...

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Published in:Entropy (Basel, Switzerland) Vol. 18; no. 10; p. 365
Main Authors: Sakaguchi, Hiromasa, Ogata, Koji, Isomura, Tetsu, Utsunomiya, Shoko, Yamamoto, Yoshihisa, Aihara, Kazuyuki
Format: Journal Article
Language:English
Published: Basel MDPI AG 01.10.2016
Subjects:
Atomic structure
coherent Ising machine
combinatorial optimization problem
degenerate optical parametric oscillator (DOPO)
Entropy
Ligands
Molecular structure
Networks
Optical Parametric Oscillators
Optimization
Sampling
structure-based drug design
ISSN:1099-4300, 1099-4300
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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.
AbstractList 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.
Author Aihara, Kazuyuki
Ogata, Koji
Sakaguchi, Hiromasa
Utsunomiya, Shoko
Yamamoto, Yoshihisa
Isomura, Tetsu
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  surname: Aihara
  fullname: Aihara, Kazuyuki
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StartPage 365
SubjectTerms Atomic structure
coherent Ising machine
combinatorial optimization problem
degenerate optical parametric oscillator (DOPO)
Entropy
Ligands
Molecular structure
Networks
Optical Parametric Oscillators
Optimization
Sampling
structure-based drug design
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