Journal of Chemical Information and Modeling

, volume 62 , issue 5 , pages 1172-1177

Pre-Exascale Computing of Protein–Ligand Binding Free Energies with Open Source Software for Drug Design

Vytautas Gapsys ¹

David F. Hahn ²

Gary Tresadern ²

David F. Mobley ³

Markus Rampp ⁴

Bert L. de Groot ¹

Hide authors affiliations Show authors affiliations: 4 affiliations

Computational Biomolecular Dynamics Group, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany |

Computational Chemistry, Janssen Research and Development, Janssen Pharmaceutica N. V., Turnhoutseweg 30, 2340 Beerse, Belgium |

Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States |

⁴

Max-Planck Computing and Data Facility, Giessenbachstrasse 2, 85748 Garching, Germany |

Publication type: Journal Article

Publication date: 2022-02-22

American Chemical Society (ACS)

Journal of Chemical Information and Modeling

scimago Q1

wos Q1

SJR: 1.467

CiteScore: 9.8

Impact factor: 5.3

ISSN: 15499596, 1549960X

DOI: 10.1021/acs.jcim.1c01445

Copy DOI

PubMed ID: 35191702

General Chemistry

Computer Science Applications

General Chemical Engineering

Library and Information Sciences

Abstract

Nowadays, drug design projects benefit from highly accurate protein-ligand binding free energy predictions based on molecular dynamics simulations. While such calculations have been computationally expensive in the past, we now demonstrate that workflows built on open source software packages can efficiently leverage pre-exascale computing resources to screen hundreds of compounds in a matter of days. We report our results of free energy calculations on a large set of pharmaceutically relevant targets assembled to reflect industrial drug discovery projects.

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Sattasathuchana Tosaporn

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15 publications, 1 369 citations, 8 reviews

h-index: 8

University of Hawaiʻi at Mānoa

Ames National Laboratory

Iowa State University

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GOST |

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GOST Copy

Gapsys V. et al. Pre-Exascale Computing of Protein–Ligand Binding Free Energies with Open Source Software for Drug Design // Journal of Chemical Information and Modeling. 2022. Vol. 62. No. 5. pp. 1172-1177.

GOST all authors (up to 50) Copy

Gapsys V., Hahn D. F., Tresadern G., Mobley D. F., Rampp M., de Groot B. L. Pre-Exascale Computing of Protein–Ligand Binding Free Energies with Open Source Software for Drug Design // Journal of Chemical Information and Modeling. 2022. Vol. 62. No. 5. pp. 1172-1177.

RIS |

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RIS Copy

TY - JOUR

DO - 10.1021/acs.jcim.1c01445

UR - https://doi.org/10.1021/acs.jcim.1c01445

TI - Pre-Exascale Computing of Protein–Ligand Binding Free Energies with Open Source Software for Drug Design

T2 - Journal of Chemical Information and Modeling

AU - Gapsys, Vytautas

AU - Hahn, David F.

AU - Tresadern, Gary

AU - Mobley, David F.

AU - Rampp, Markus

AU - de Groot, Bert L.

PY - 2022

DA - 2022/02/22

PB - American Chemical Society (ACS)

SP - 1172-1177

IS - 5

VL - 62

PMID - 35191702

SN - 1549-9596

SN - 1549-960X

ER -

BibTex |

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BibTex (up to 50 authors) Copy

@article{2022_Gapsys,

author = {Vytautas Gapsys and David F. Hahn and Gary Tresadern and David F. Mobley and Markus Rampp and Bert L. de Groot},

title = {Pre-Exascale Computing of Protein–Ligand Binding Free Energies with Open Source Software for Drug Design},

journal = {Journal of Chemical Information and Modeling},

year = {2022},

volume = {62},

publisher = {American Chemical Society (ACS)},

month = {feb},

url = {https://doi.org/10.1021/acs.jcim.1c01445},

number = {5},

pages = {1172--1177},

doi = {10.1021/acs.jcim.1c01445}

}

MLA

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MLA Copy

Gapsys, Vytautas, et al. “Pre-Exascale Computing of Protein–Ligand Binding Free Energies with Open Source Software for Drug Design.” Journal of Chemical Information and Modeling, vol. 62, no. 5, Feb. 2022, pp. 1172-1177. https://doi.org/10.1021/acs.jcim.1c01445.

Publisher

American Chemical Society (ACS)

Journal

Journal of Chemical Information and Modeling

scimago Q1

wos Q1

SJR

1.467

CiteScore

9.8

Impact factor

5.3

ISSN

15499596 (Print)

1549960X (Electronic)