Scoring protein-ligand binding structures through learning atomic graphs with inter-molecular adjacency.

Authors

Debby D Wang, Yuting Huang

Published in

PLoS computational biology. Volume 21. Issue 5. Pages e1013074. May 09, 2025. Epub May 09, 2025.

Abstract

With a burgeoning number of artificial intelligence (AI) applications in various fields, biomolecular science has also given a big welcome to advanced AI techniques in recent years. In this broad field, scoring a protein-ligand binding structure to output the binding strength is a crucial problem that heavily relates to computational drug discovery. Aiming at this problem, we have proposed an efficient scoring framework using deep learning techniques. This framework describes a binding structure by a high-resolution atomic graph, places a focus on the inter-molecular interactions and learns the graph in a rational way. For a protein-ligand binding complex, the generated atomic graph reserves key information of the atoms (as graph nodes), and focuses on inter-molecular interactions (as graph edges) that can be identified by introducing multiple distance ranges to the atom pairs within the binding area. To provide more confidence in the predicted binding strengths, we have interpreted the deep learning model from the model level and in a post-hoc analysis. The proposed learning framework has been demonstrated to have competitive performances in scoring and screening tasks, which will prospectively promote the development of related fields further.

PMID:
40344574
Bibliographic data and abstract were imported from PubMed on 10 May 2025.

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