Issue 5, 2024

Towards equilibrium molecular conformation generation with GFlowNets

Abstract

Sampling diverse, thermodynamically feasible molecular conformations plays a crucial role in predicting properties of a molecule. In this paper we propose to use GFlowNets for sampling conformations of small molecules from the Boltzmann distribution, as determined by the molecule's energy. The proposed approach can be used in combination with energy estimation methods of different fidelity and discovers a diverse set of low-energy conformations for drug-like molecules. We demonstrate that GFlowNets can reproduce molecular potential energy surfaces by sampling proportionally to the Boltzmann distribution.

Graphical abstract: Towards equilibrium molecular conformation generation with GFlowNets

Transparent peer review

To support increased transparency, we offer authors the option to publish the peer review history alongside their article.

View this article’s peer review history

Article information

Article type
Paper
Submitted
15 Jan 2024
Accepted
22 Mar 2024
First published
29 Apr 2024
This article is Open Access
Creative Commons BY-NC license

Digital Discovery, 2024,3, 1038-1047

Towards equilibrium molecular conformation generation with GFlowNets

A. Volokhova, M. Koziarski, A. Hernández-García, C. Liu, S. Miret, P. Lemos, L. Thiede, Z. Yan, A. Aspuru-Guzik and Y. Bengio, Digital Discovery, 2024, 3, 1038 DOI: 10.1039/D4DD00023D

This article is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported Licence. You can use material from this article in other publications, without requesting further permission from the RSC, provided that the correct acknowledgement is given and it is not used for commercial purposes.

To request permission to reproduce material from this article in a commercial publication, please go to the Copyright Clearance Center request page.

If you are an author contributing to an RSC publication, you do not need to request permission provided correct acknowledgement is given.

If you are the author of this article, you do not need to request permission to reproduce figures and diagrams provided correct acknowledgement is given. If you want to reproduce the whole article in a third-party commercial publication (excluding your thesis/dissertation for which permission is not required) please go to the Copyright Clearance Center request page.

Read more about how to correctly acknowledge RSC content.

Social activity

Spotlight

Advertisements