ET-Flow: Equivariant Flow-Matching for Molecular Conformer Generation

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 thatdiffuse over conformer fields, or use computationally expensive methods to gen-erate initial structures and diffuse over torsion angles. In this work, we introduceEquivariant Transformer Flow (ET-Flow). We showcase that a well-designedflow matching approach with equivariance and harmonic prior alleviates the needfor complex internal geometry calculations and large architectures, contrary tothe prevailing methods in the field. Our approach results in a straightforwardand scalable method that directly operates on all-atom coordinates with minimalassumptions. With the advantages of equivariance and flow matching, ET-Flowsignificantly increases the precision and physical validity of the generated con-formers, while being a lighter model and faster at inference. Code is availablehttps://github.com/shenoynikhil/ETFlow.