Towards equilibrium molecular conformation generation with GFlowNets

Alexandra Volokhova, Michał Koziarski, Alex Hernández-García, Cheng-Hao Liu, Santiago Miret, Pablo Lemos, Luca Thiede, Zichao Yan, Alan Aspuru-Guzik, Yoshua Bengio

Submission Track: Papers

Submission Category: AI-Guided Design

Keywords: molecular conformation generation, GFlowNet, Boltzmann generator

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.

Digital Discovery Special Issue: Yes

Submission Number: 85