Equivariant Flow Matching for Molecular Conformer Generation

Majdi Hassan, Nikhil Shenoy, Jungyoon Lee, Hannes Stark, Stephan Thaler, Dominique Beaini

Keywords: flow matching, molecular conformers, equivariant graph networks

TL;DR: We leverage flow matching and equivariant graph networks to state-of-the-art performance on generating conformers.

Abstract: Predicting low-energy molecular conformations given a molecular graph is an important but challenging task in computational drug discovery. Existing state-of-the-art approaches either resort to large scale transformer-based models that diffuse over conformer fields, or use computationally expensive methods to generate initial structures and diffuse over torsion angles. In this work, we introduce Equivariant Transformer Flow (ET-Flow). We showcase that a well-designed flow matching approach with equivariance and harmonic prior alleviates the need for complex internal geometry calculations and large architectures, contrary to the prevailing methods in the field. Our approach results in a straightforward and scalable method that directly operates on all-atom coordinates with minimal assumptions. ET-Flow outperforms or matches the previous state-of-the-art in molecular conformer generation benchmarks with significantly fewer parameters, no dependence on internal geometry, and fast inference.

Submission Number: 36