TRIDS: AI-native molecular docking framework for accelerating high-throughput virtual screening with physically valid binding poses

Abstract

Molecular docking is a cornerstone of drug discovery for unveiling the mechanism of ligand-receptor interactions. With the recent advances of deep learning (DL), AI-powered molecular docking methods have achieved higher accuracy for binding pose prediction and virtual screening compared with classical physics-based methods. However, there is still a scarcity of approaches to strike a balance among accuracy, computational efficiency, and rigorous physical validity of the output conformations. In the previous two versions of DSDP, we demonstrated the effectiveness of guiding conformation sampling with the gradient of an analytic scoring function. As the third version, TRIDS was devised as an AI-native docking framework that expand the similar strategy to unify conformation sampling and docking processes with DL-based model for improving accuracy of docking and screening. Furthermore, it is tailored for seamless cooperation of AI and physics to guarantee the physical validity of predicted binding poses. Being user-friendly, TRIDS predicts the binding site, parses multiple file formats, and supports Python programming and PyMOL graphical interaction. It improves docking accuracy and passes physical validation with high computational efficiency, i.e. a single docking task is done in a fraction of second while maintaining a highly lightweight GPU memory footprint of merely hundreds of megabytes, facilitating high-throughput virtual screening in reality. As a proof of concept, TRIDS allowed us to obtain hit compounds with novel scaffolds for tumor necrosis factor-alpha (TNFα) inhibitor through a large-scale virtual screening.