Predicting Affinity Through Homology (PATH): Interpretable binding affinity prediction with persistent homology

Yuxi Long; Bruce R. Donald

doi:10.1371/journal.pcbi.1013216

Loading metrics

Open Access

Peer-reviewed

Research Article

Predicting Affinity Through Homology (PATH): Interpretable binding affinity prediction with persistent homology

Yuxi Long,

Roles Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Software, Validation, Visualization, Writing – original draft, Writing – review & editing

Affiliation Department of Computer Science, Department of Mathematics, Duke University, Durham, North Carolina, United States of America
⨯
Bruce R. Donald

Roles Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Resources, Software, Supervision, Validation, Visualization, Writing – original draft, Writing – review & editing

* E-mail: brd+pcb25@cs.duke.edu

Affiliations Department of Computer Science, Department of Mathematics, Duke University, Durham, North Carolina, United States of America, Department of Biochemistry, Department of Chemistry, Duke University and Duke University School of Medicine, Durham, North Carolina, United States of America

https://orcid.org/0000-0001-6884-4398

⨯

Predicting Affinity Through Homology (PATH): Interpretable binding affinity prediction with persistent homology

Yuxi Long,
Bruce R. Donald

Published: June 27, 2025
https://doi.org/10.1371/journal.pcbi.1013216

About the Authors

Yuxi Long

Roles Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Software, Validation, Visualization, Writing – original draft, Writing – review & editing

Affiliation Department of Computer Science, Department of Mathematics, Duke University, Durham, North Carolina, United States of America

Bruce R. Donald

Roles Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Resources, Software, Supervision, Validation, Visualization, Writing – original draft, Writing – review & editing

* E-mail: brd+pcb25@cs.duke.edu

Affiliations Department of Computer Science, Department of Mathematics, Duke University, Durham, North Carolina, United States of America, Department of Biochemistry, Department of Chemistry, Duke University and Duke University School of Medicine, Durham, North Carolina, United States of America

https://orcid.org/0000-0001-6884-4398

Competing Interests

I have read the journal’s policy and the authors of this manuscript have the following competing interests: B.R.D. is a founder of Ten63 Therapeutics, Inc. B.R.D. was previously a guest editor for PLoS Comp. Biol.

Subject Areas
?

For more information about PLOS Subject Areas, click here.
We want your feedback. Do these Subject Areas make sense for this article? Click the target next to the incorrect Subject Area and let us know. Thanks for your help!

Machine learning algorithms
Is the Subject Area "Machine learning algorithms" applicable to this article?

Thanks for your feedback.
Decision trees
Is the Subject Area "Decision trees" applicable to this article?

Thanks for your feedback.
Algorithms
Is the Subject Area "Algorithms" applicable to this article?

Thanks for your feedback.
Deep learning
Is the Subject Area "Deep learning" applicable to this article?

Thanks for your feedback.
Proteases
Is the Subject Area "Proteases" applicable to this article?

Thanks for your feedback.
Neural networks
Is the Subject Area "Neural networks" applicable to this article?

Thanks for your feedback.
Protein interactions
Is the Subject Area "Protein interactions" applicable to this article?

Thanks for your feedback.
Proteomic databases
Is the Subject Area "Proteomic databases" applicable to this article?

Thanks for your feedback.