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Poster

Group Ligands Docking to Protein Pockets

Jiaqi Guan · Jiahan Li · Xiangxin Zhou · Xingang Peng · Sheng Wang · Yunan Luo · Jian Peng · Jianzhu Ma

Hall 3 + Hall 2B #8
[ ]
Thu 24 Apr midnight PDT — 2:30 a.m. PDT

Abstract:

Molecular docking is a key task in computational biology that has attracted increasing interest from the machine learning community. While existing methods have achieved success, they generally treat each protein-ligand pair in isolation. Inspired by the biochemical observation that ligands binding to the same target protein tend to adopt similar poses, we propose \textsc{GroupBind}, a novel molecular docking framework that simultaneously considers multiple ligands docking to a protein. This is achieved by introducing an interaction layer for the group of ligands and a triangle attention module for embedding protein-ligand and group-ligand pairs. By integrating our approach with diffusion based docking model, we set a new state-of-the-art performance on the PDBBind blind docking benchmark, demonstrating the effectiveness of our paradigm in enhancing molecular docking accuracy.

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