A molecular video-derived foundation model for scientific drug discovery

Abstract

Accurate molecular representation of compounds is a fundamental challenge for prediction of drug targets and molecular properties. In this study, we present a molecular video-based foundation model, named VideoMol, pretrained on 120 million frames of 2 million unlabeled drug-like and bioactive molecules. VideoMol renders each molecule as a video with 60-frame and designs three self-supervised learning strategies on molecular videos to capture molecular representation. We show high performance of VideoMol in predicting molecular targets and properties across 43 drug discovery benchmark datasets. VideoMol achieves high accuracy in identifying antiviral molecules against common diverse disease-specific drug targets (i.e., BACE1 and EP4). Drugs screened by VideoMol show better binding affinity than molecular docking, revealing the effectiveness in understanding the three-dimensional structure of molecules. We further illustrate interpretability of VideoMol using key chemical substructures.