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Towards equilibrium molecular conformation generation with GFlowNets

20 October 2023
Alexandra Volokhova
Michal Koziarski
Alex Hernández-García
Cheng-Hao Liu
Santiago Miret
Pablo Lemos
Luca Thiede
Zichao Yan
Alán Aspuru-Guzik
Yoshua Bengio
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Abstract

Sampling diverse, thermodynamically feasible molecular conformations plays a crucial role in predicting properties of a molecule. In this paper we propose to use GFlowNet 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 highly flexible drug-like molecules. We demonstrate that GFlowNet can reproduce molecular potential energy surfaces by sampling proportionally to the Boltzmann distribution.

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