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Title: Dowker complex based machine learning (DCML) models for protein-ligand binding affinity prediction
Authors: Liu, Xiang
Feng, Huitao
Wu, Jie
Xia, Kelin
Keywords: Science::Mathematics
Issue Date: 2022
Source: Liu, X., Feng, H., Wu, J. & Xia, K. (2022). Dowker complex based machine learning (DCML) models for protein-ligand binding affinity prediction. PLOS Computational Biology, 18(4), e1009943-.
Project: M4081842
Journal: PLOS Computational Biology
Abstract: With the great advancements in experimental data, computational power and learning algorithms, artificial intelligence (AI) based drug design has begun to gain momentum recently. AI-based drug design has great promise to revolutionize pharmaceutical industries by significantly reducing the time and cost in drug discovery processes. However, a major issue remains for all AI-based learning model that is efficient molecular representations. Here we propose Dowker complex (DC) based molecular interaction representations and Riemann Zeta function based molecular featurization, for the first time. Molecular interactions between proteins and ligands (or others) are modeled as Dowker complexes. A multiscale representation is generated by using a filtration process, during which a series of DCs are generated at different scales. Combinatorial (Hodge) Laplacian matrices are constructed from these DCs, and the Riemann zeta functions from their spectral information can be used as molecular descriptors. To validate our models, we consider protein-ligand binding affinity prediction. Our DC-based machine learning (DCML) models, in particular, DC-based gradient boosting tree (DC-GBT), are tested on three most-commonly used datasets, i.e., including PDBbind-2007, PDBbind-2013 and PDBbind-2016, and extensively compared with other existing state-of-the-art models. It has been found that our DC-based descriptors can achieve the state-of-the-art results and have better performance than all machine learning models with traditional molecular descriptors. Our Dowker complex based machine learning models can be used in other tasks in AI-based drug design and molecular data analysis.
ISSN: 1553-734X
DOI: 10.1371/journal.pcbi.1009943
Schools: School of Physical and Mathematical Sciences 
Rights: © 2022 Liu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Fulltext Permission: open
Fulltext Availability: With Fulltext
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