3D Molecular Generation via Virtual Dynamics

Abstract

Structure-based drug design, a critical aspect of drug discovery, aims to identify high-affinity molecules for target protein pockets. Traditional virtual screening methods, which involve exhaustive searches within large molecular databases, are inefficient and limited in discovering novel molecules. The pocket-based 3D molecular generation model offers a promising alternative by directly generating molecules with 3D structures and binding positions in the pocket. In this paper, we present VD-Gen, a novel pocket-based 3D molecular generation pipeline. VD-Gen features a series of carefully designed stages to generate fine-grained 3D molecules with binding positions in the pocket cavity end-to-end. Rather than directly generating or sampling atoms with 3D positions in the pocket, VD-Gen randomly initializes multiple virtual particles within the pocket and learns to iteratively move them to approximate the distribution of molecular atoms in 3D space. After the iterative movement, a 3D molecule is extracted and further refined through additional iterative movement, yielding a high-quality 3D molecule with a confidence score. Comprehensive experimental results on pocket-based molecular generation demonstrate that VD-Gen can generate novel 3D molecules that fill the target pocket cavity with high binding affinities, significantly outperforming previous baselines.