APMG: 3D Molecule Generation Driven by Atomic Chemical Properties

Abstract

Recently, mask-fill-based 3D Molecular Generation (MG) methods have become very popular in virtual drug design. However, the existing MG methods ignore the chemical properties of atoms and contain inappropriate atomic position training data, which limits their generation capability. To mitigate the above issues, this paper presents a novel mask-fill-based 3D molecule generation model driven by atomic chemical properties (APMG). Specifically, we construct a new attention-MPNN-based encoder and introduce the electronic information into atom representations to enrich chemical properties. Also, a multi-functional classifier is designed to predict the electronic information of each generated atom, guiding the type prediction of elements and bonds. By design, the proposed method uses the chemical properties of atoms and their correlations for high-quality molecule generation. Second, to optimize the atomic position training data, we propose a novel atomic training position generation approach using the Chi-Square distribution. We evaluate our APMG method on the CrossDocked dataset and visualize the docking states of the pockets and generated molecules. The obtained results demonstrate the superiority and merits of APMG over the state-of-the-art approaches.