Forman persistent Ricci curvature (FPRC)-based machine learning models for protein–ligand binding affinity prediction

JJ Wee, K Xia - Briefings in Bioinformatics, 2021 - academic.oup.com
Artificial intelligence (AI) techniques have already been gradually applied to the entire drug
design process, from target discovery, lead discovery, lead optimization and preclinical …

Ollivier persistent Ricci curvature-based machine learning for the protein–ligand binding affinity prediction

JJ Wee, K Xia - Journal of Chemical Information and Modeling, 2021 - ACS Publications
Efficient molecular featurization is one of the major issues for machine learning models in
drug design. Here, we propose a persistent Ricci curvature (PRC), in particular, Ollivier PRC …

Molecular persistent spectral image (Mol-PSI) representation for machine learning models in drug design

P Jiang, Y Chi, XS Li, Z Meng, X Liu… - Briefings in …, 2022 - academic.oup.com
Artificial intelligence (AI)-based drug design has great promise to fundamentally change the
landscape of the pharmaceutical industry. Even though there are great progress from …

Persistent spectral–based machine learning (PerSpect ML) for protein-ligand binding affinity prediction

Z Meng, K Xia - Science advances, 2021 - science.org
Molecular descriptors are essential to not only quantitative structure-activity relationship
(QSAR) models but also machine learning–based material, chemical, and biological data …

[HTML][HTML] Structure-based protein–ligand interaction fingerprints for binding affinity prediction

DD Wang, MT Chan, H Yan - Computational and Structural Biotechnology …, 2021 - Elsevier
Binding affinity prediction (BAP) using protein–ligand complex structures is crucial to
computer-aided drug design, but remains a challenging problem. To achieve efficient and …

Persistent spectral based ensemble learning (PerSpect-EL) for protein–protein binding affinity prediction

JJ Wee, K Xia - Briefings in Bioinformatics, 2022 - academic.oup.com
Protein–protein interactions (PPIs) play a significant role in nearly all cellular and biological
activities. Data-driven machine learning models have demonstrated great power in PPIs …

[HTML][HTML] BiComp-DTA: Drug-target binding affinity prediction through complementary biological-related and compression-based featurization approach

M Kalemati, M Zamani Emani… - PLOS Computational …, 2023 - journals.plos.org
Drug-target binding affinity prediction plays a key role in the early stage of drug discovery.
Numerous experimental and data-driven approaches have been developed for predicting …

Hypergraph-based persistent cohomology (HPC) for molecular representations in drug design

X Liu, X Wang, J Wu, K Xia - Briefings in Bioinformatics, 2021 - academic.oup.com
Artificial intelligence (AI) based drug design has demonstrated great potential to
fundamentally change the pharmaceutical industries. Currently, a key issue in AI-based drug …

Persistent path-spectral (PPS) based machine learning for protein–ligand binding affinity prediction

R Liu, X Liu, J Wu - Journal of Chemical Information and Modeling, 2023 - ACS Publications
Molecular descriptors are essential to quantitative structure activity/property relationship
(QSAR/QSPR) models and machine learning models. Here we propose persistent path …

[HTML][HTML] SMPLIP-Score: predicting ligand binding affinity from simple and interpretable on-the-fly interaction fingerprint pattern descriptors

S Kumar, M Kim - Journal of cheminformatics, 2021 - Springer
In drug discovery, rapid and accurate prediction of protein–ligand binding affinities is a
pivotal task for lead optimization with acceptable on-target potency as well as …