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Position Papers of the 19th Conference on Computer Science and Intelligence Systems

Annals of Computer Science and Information Systems, Volume 40

A generic method of pose generation in molecular docking via quadratic unconstrained binary optimization

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DOI: http://dx.doi.org/10.15439/2024F3588

Citation: Position Papers of the 19th Conference on Computer Science and Intelligence Systems, M. Bolanowski, M. Ganzha, L. Maciaszek, M. Paprzycki, D. Ślęzak (eds). ACSIS, Vol. 40, pages 69–71 ()

Full text

Abstract. Docking of a ligand onto the binding pocket of its protein target, designated as the molecular docking problem, is a very important method for structure-based drug design. We have implemented a generic pose generation method for molecular docking by solving the quadratic unconstrained binary optimization (QUBO) problem with the Fujitsu digital annealer. In combination with the AutoDock 4 scoring function, the success rate for predicting the binding poses to be sufficiently close to their experimental binding poses, namely, with the root mean squared deviation (RMSD) less than 2 Å, was 84.3 \%, when benchmarking against part of the PDBbind core set (242 protein-ligand complexes). To our best knowledge, this is the first implementation of molecular docking that conforms with the QUBO formalism demonstrating a performance comparable with the conventional methods.

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