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

doi:10.1109/iciibms55689.2022.9971653

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

College of Engineering and Physical Sciences

Research output: Chapter in Book/Published conference output › Conference 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 language	English
Title of host publication	ICIIBMS 2022 - 7th International Conference on Intelligent Informatics and Biomedical Sciences
Publisher	IEEE
Pages	241-242
ISBN (Electronic)	9781665482295
DOIs	https://doi.org/10.1109/iciibms55689.2022.9971653
Publication status	Published - 24 Nov 2022
Event	7th International Conference on Intelligent Informatics and Biomedical Sciences, ICIIBMS 2022 - Nara, Japan Duration: 24 Nov 2022 → 26 Nov 2022

Publication series

Name	International Conference on Intelligent Informatics and Biomedical Science (ICIIBMS)
Publisher	IEEE

Conference

Conference	7th International Conference on Intelligent Informatics and Biomedical Sciences, ICIIBMS 2022
Country/Territory	Japan
City	Nara
Period	24/11/22 → 26/11/22

Keywords

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

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10.1109/iciibms55689.2022.9971653

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Postnikov, E. B., Maximova, E., Farafonov, V., Lavrova, A. I., & Nerukh, D. (2022). Statistical criteria for quantitative prediction of protein-ligand dissociation rate using all-atom Molecular Dynamics. In ICIIBMS 2022 - 7th International Conference on Intelligent Informatics and Biomedical Sciences (pp. 241-242). (International Conference on Intelligent Informatics and Biomedical Science (ICIIBMS)). IEEE. https://doi.org/10.1109/iciibms55689.2022.9971653

Postnikov, Eugene B. ; Maximova, Ekaterina ; Farafonov, Vladimir et al. / Statistical criteria for quantitative prediction of protein-ligand dissociation rate using all-atom Molecular Dynamics. ICIIBMS 2022 - 7th International Conference on Intelligent Informatics and Biomedical Sciences. IEEE, 2022. pp. 241-242 (International Conference on Intelligent Informatics and Biomedical Science (ICIIBMS)).

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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.",

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author = "Postnikov, {Eugene B.} and Ekaterina Maximova and Vladimir Farafonov and Lavrova, {Anastasia I.} and Dmitry Nerukh",

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Postnikov, EB, Maximova, E, Farafonov, V, Lavrova, AI & Nerukh, D 2022, Statistical criteria for quantitative prediction of protein-ligand dissociation rate using all-atom Molecular Dynamics. in ICIIBMS 2022 - 7th International Conference on Intelligent Informatics and Biomedical Sciences. International Conference on Intelligent Informatics and Biomedical Science (ICIIBMS), IEEE, pp. 241-242, 7th International Conference on Intelligent Informatics and Biomedical Sciences, ICIIBMS 2022, Nara, Japan, 24/11/22. https://doi.org/10.1109/iciibms55689.2022.9971653

Statistical criteria for quantitative prediction of protein-ligand dissociation rate using all-atom Molecular Dynamics. / Postnikov, Eugene B.; Maximova, Ekaterina; Farafonov, Vladimir et al.
ICIIBMS 2022 - 7th International Conference on Intelligent Informatics and Biomedical Sciences. IEEE, 2022. p. 241-242 (International Conference on Intelligent Informatics and Biomedical Science (ICIIBMS)).

Research output: Chapter in Book/Published conference output › Conference publication

TY - GEN

T1 - Statistical criteria for quantitative prediction of protein-ligand dissociation rate using all-atom Molecular Dynamics

AU - Postnikov, Eugene B.

AU - Maximova, Ekaterina

AU - Farafonov, Vladimir

AU - Lavrova, Anastasia I.

AU - Nerukh, Dmitry

PY - 2022/11/24

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N2 - 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.

AB - 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.

KW - Protein-ligand dissociation

KW - all-atom

KW - molecular dynamics

KW - τ-RAMD

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Postnikov EB, Maximova E, Farafonov V, Lavrova AI, Nerukh D. Statistical criteria for quantitative prediction of protein-ligand dissociation rate using all-atom Molecular Dynamics. In ICIIBMS 2022 - 7th International Conference on Intelligent Informatics and Biomedical Sciences. IEEE. 2022. p. 241-242. (International Conference on Intelligent Informatics and Biomedical Science (ICIIBMS)). doi: 10.1109/iciibms55689.2022.9971653

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

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