REBIND: Enhancing Ground-state Molecular Conformation Prediction via Force-Based Graph Rewiring

Taewon Kim, Hyunjin Seo, Sungsoo Ahn, Eunho Yang

Keywords: molecular conformation prediction, molecule modeling, graph neural network

Abstract: Predicting the ground-state 3D molecular conformations from 2D molecular graphs is critical in computational chemistry due to its profound impact on molecular properties. Deep learning (DL) approaches have recently emerged as promising alternatives to computationally-heavy classical methods such as density functional theory (DFT). However, we discover that existing DL methods inadequately model inter-atomic forces, particularly for non-bonded atomic pairs, due to their naive usage of bonds and pairwise distances. Consequently, significant prediction errors occur for atoms with low degree (*i.e.*, low coordination numbers) whose conformations are primarily influenced by non-bonded interactions. To address this, we propose **ReBind**, a novel framework that rewires molecular graphs by adding edges based on the Lennard-Jones potential to capture non-bonded interactions for low-degree atoms. Experimental results demonstrate that **ReBind** significantly outperforms state-of-the-art methods across various molecular sizes, achieving up to a 20% reduction in prediction error.

Primary Area: applications to physical sciences (physics, chemistry, biology, etc.)

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Submission Number: 4569