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

Kursk State University,Department of Theoretical Physics,Kursk,Russia
Technische Universität Dresden,Center for Molecular and Cellular Bioengineering,Dresden,Germany
Department of Physical Chemistry, V. N. Karazin Kharkiv National University, Svobody Sq. 4, Kharkiv, 61022, Ukraine.
Saint-Petersburg State University,Saint-Petersburg State Research Institute of Phthisiopulmonology,Saint-Petersburg,Russia

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

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.",

keywords = "Protein-ligand dissociation, all-atom, molecular dynamics, τ-RAMD",

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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

Y1 - 2022/11/24

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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BT - ICIIBMS 2022 - 7th International Conference on Intelligent Informatics and Biomedical Sciences

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T2 - 7th International Conference on Intelligent Informatics and Biomedical Sciences, ICIIBMS 2022

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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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