Machine learning prediction of inter-fragment interaction energies between ligand and amino-acid residues on the fragment molecular orbital calculations for Janus kinase – inhibitor complex

Shusuke Tokutomi, Kohei Shimamura, Kaori Fukuzawa, Shigenori Tanaka

Research output: Contribution to journalArticlepeer-review

Abstract

Inter-Fragment Interaction Energies (IFIEs) obtained by Fragment Molecular Orbital (FMO) method can quantitatively measure the effective interactions between ligand and residues in protein, which are therefore useful for drug discovery. However, it has not been clarified whether the IFIEs can be reproduced using only geometrical (e.g., interatomic distances) information of biomolecular complex without resort to explicit FMO calculations. In this study, through machine learning technique, we propose a highly accurate reproduction or prediction scheme for ligand-protein IFIEs using only the distance information as descriptors, thereby drastically saving the computational cost in FMO analysis for a variety of conformations.

Original languageEnglish
Article number137883
JournalChemical Physics Letters
Volume757
DOIs
Publication statusPublished - 2020 Oct 16
Externally publishedYes

Keywords

  • Fragment molecular orbital method (FMO)
  • Inter-fragment interaction energy (IFIE)
  • Janus kinase (JAK)
  • Ligand-protein complex
  • Machine learning

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

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