A multi-perspective model for protein–ligand-binding affinity prediction

Xianfeng ZHANG, Yafei LI, Jinlan WANG, Guandong XU, Yanhui GU

Research output: Contribution to journalArticlespeer-review


Gathering information from multi-perspective graphs is an essential issue for many applications especially for protein–ligand-binding affinity prediction. Most of traditional approaches obtained such information individually with low interpretability. In this paper, we harness the rich information from multi-perspective graphs with a general model, which abstractly represents protein–ligand complexes with better interpretability while achieving excellent predictive performance. In addition, we specially analyze the protein–ligand-binding affinity problem, taking into account the heterogeneity of proteins and ligands. Experimental evaluations demonstrate the effectiveness of our data representation strategy on public datasets by fusing information from different perspectives. All codes are available in the https://github.com/Jthy-af/HaPPy. Copyright © 2023 International Association of Scientists in the Interdisciplinary Areas.

Original languageEnglish
Pages (from-to)696-709
JournalInterdisciplinary Sciences: Computational Life Sciences
Early online dateOct 2023
Publication statusPublished - Dec 2023


Zhang, X., Li, Y., Wang, J., Xu, G., & Gu, Y. (2023). A multi-perspective model for protein–ligand-binding affinity prediction. Interdisciplinary Sciences: Computational Life Sciences, 15, 696-709. https://doi.org/10.1007/s12539-023-00582-y


  • Binding affinity prediction
  • Data representation
  • Graph neural network
  • Protein language model


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