Journal
ENTROPY
Volume 18, Issue 10, Pages -Publisher
MDPI
DOI: 10.3390/e18100365
Keywords
degenerate optical parametric oscillator (DOPO); structure-based drug design; coherent Ising machine; combinatorial optimization problem
Categories
Funding
- Impulsing Paradigm Change through Disruptive Technologies (ImPACT) Program of the Council of Science, Technology and Innovation
- Grants-in-Aid for Scientific Research [15H05707] Funding Source: KAKEN
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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.
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