Proteo-chemometrics interaction fingerprints of protein-ligand complexes predict binding affinity

Debby D WANG*, Haoran XIE, Hong YAN

*Corresponding author for this work

Research output: Journal PublicationsJournal Article (refereed)peer-review

7 Citations (Scopus)


Motivation: Reliable predictive models of protein-ligand binding affinity are required in many areas of biomedical research. Accurate prediction based on current descriptors or molecular fingerprints (FPs) remains a challenge. We develop novel interaction FPs (IFPs) to encode protein-ligand interactions and use them to improve the prediction. Results: Proteo-chemometrics IFPs (PrtCmm IFPs) formed by combining extended connectivity fingerprints (ECFPs) with the proteo-chemometrics concept. Combining PrtCmm IFPs with machine-learning models led to efficient scoring models, which were validated on the PDBbind v2019 core set and CSAR-HiQ sets. The PrtCmm IFP Score outperformed several other models in predicting protein-ligand binding affinities. Besides, conventional ECFPs were simplified to generate new IFPs, which provided consistent but faster predictions. The relationship between the base atom properties of ECFPs and the accuracy of predictions was also investigated.

Original languageEnglish
Article number17
Pages (from-to)2570-2579
Number of pages10
Issue number17
Early online date26 Feb 2021
Publication statusPublished - 1 Sept 2021

Bibliographical note

This work has been supported by the Hong Kong Innovation and Technology Commission, the Hong Kong Research Grants Council [Project 11200818] and City University of Hong Kong [Project 9610460].

Supplementary information
Supplementary data are available at Bioinformatics online.

© The Author(s) (2021). Published by Oxford University Press. All rights reserved. For Permissions, please email:


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