Leveraging Side Information for Ligand Conformation Generation using Diffusion-Based Approaches

TL;DR

This paper introduces SIDEGEN, a diffusion-based method that leverages side information and message passing to generate biologically relevant ligand conformations, significantly improving accuracy over existing models.

Contribution

The paper presents a novel diffusion model incorporating side information and message passing for ligand conformation generation, enhancing biological relevance and accuracy.

Findings

Outperforms GeoDiff by 20% in median aligned RMSD

Improves ligand conformation quality on PDBBind-2020 dataset

Incorporates target features and non-covalent interactions effectively

Abstract

Ligand molecule conformation generation is a critical challenge in drug discovery. Deep learning models have been developed to tackle this problem, particularly through the use of generative models in recent years. However, these models often generate conformations that lack meaningful structure and randomness due to the absence of essential side information. Examples of such side information include the chemical and geometric features of the target protein, ligand-target compound interactions, and ligand chemical properties. Without these constraints, the generated conformations may not be suitable for further selection and design of new drugs. To address this limitation, we propose a novel method for generating ligand conformations that leverage side information and incorporate flexible constraints into standard diffusion models. Drawing inspiration from the concept of message passing, we introduce ligand-target massage passing block, a mechanism that facilitates the exchange of information between target nodes and ligand nodes, thereby incorporating target node features. To capture non-covalent interactions, we introduce ligand-target compound inter and intra edges. To further improve the biological relevance of the generated conformations, we train energy models using scalar chemical features. These models guide the progress of the standard Denoising Diffusion Probabilistic Models, resulting in more biologically meaningful conformations. We evaluate the performance of SIDEGEN using the PDBBind-2020 dataset, comparing it against other methods. The results demonstrate improvements in both Aligned RMSD and Ligand RMSD evaluations. Specifically, our model outperforms GeoDiff (trained on PDBBind-2020) by 20% in terms of the median aligned RMSD metric.