GLProtein: Global-and-Local Structure Aware Protein Representation Learning

ACL ARR 2025 May Submission3476 Authors

Abstract: Proteins are central to biological systems, participating as building blocks across all forms of life. Despite advancements in understanding protein functions through protein sequence analysis, there remains potential for further exploration in integrating protein structural information. We argue that the structural information of proteins is not only limited to their 3D information but also encompasses information from amino acid molecules (local information) to protein-protein structure similarity (global information). To address this, we propose GLProtein, the first framework in protein pre-training that incorporates both global structural similarity and local amino acid details to enhance prediction accuracy and functional insights. GLProtein innovatively combines protein-masked modelling with triplet structure similarity scoring, protein 3D distance encoding and substructure-based amino acid molecule encoding. Experimental results demonstrate that GLProtein outperforms previous methods in several bioinformatics tasks, including predicting protein-protein interactions, contact prediction, and so on.

Paper Type: Long

Research Area: Language Modeling

Research Area Keywords: applications; pre-training

Contribution Types: Model analysis & interpretability, NLP engineering experiment, Publicly available software and/or pre-trained models

Languages Studied: English

Submission Number: 3476