Statistical criteria for quantitative prediction of protein-ligand dissociation rate using all-atom Molecular Dynamics

Eugene B. Postnikov, Ekaterina Maximova, Vladimir Farafonov, Anastasia I. Lavrova, Dmitry Nerukh

Research output: Chapter in Book/Published conference outputConference publication

Abstract

We have recently demonstrated [J. Chem. Phys. Lett. 12 (2021) 10631] that a proper modification of the Kramers reaction rate model can be used for quantitative estimation of the protein-ligand dissociation rate constant from all-atom random accelerated Molecular Dynamics (τ-RAMD) data. This procedure requires extrapolation of the results obtained in the picoseconds interval to the values in the seconds range. Here, we report a statistical procedure for such extrapolation, which provides analytical estimations of the uncertainty in the obtained dissociation rate. The validity of the procedure is illustrated by a new, larger MD dataset.
Original languageEnglish
Title of host publicationICIIBMS 2022 - 7th International Conference on Intelligent Informatics and Biomedical Sciences
PublisherIEEE
Pages241-242
ISBN (Electronic)9781665482295
DOIs
Publication statusPublished - 24 Nov 2022
Event7th International Conference on Intelligent Informatics and Biomedical Sciences, ICIIBMS 2022 - Nara, Japan
Duration: 24 Nov 202226 Nov 2022

Publication series

NameInternational Conference on Intelligent Informatics and Biomedical Science (ICIIBMS)
PublisherIEEE

Conference

Conference7th International Conference on Intelligent Informatics and Biomedical Sciences, ICIIBMS 2022
Country/TerritoryJapan
CityNara
Period24/11/2226/11/22

Keywords

  • Protein-ligand dissociation
  • all-atom
  • molecular dynamics
  • τ-RAMD

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