[HTML][HTML] Machine learning small molecule properties in drug discovery

N Schapin, M Majewski, A Varela-Rial, C Arroniz… - Artificial Intelligence …, 2023 - Elsevier
Abstract Machine learning (ML) is a promising approach for predicting small molecule
properties in drug discovery. Here, we provide a comprehensive overview of various ML …

Modern machine‐learning for binding affinity estimation of protein–ligand complexes: Progress, opportunities, and challenges

T Harren, T Gutermuth, C Grebner… - Wiley …, 2024 - Wiley Online Library
Abstract Structure‐based drug design is a widely applied approach in the discovery of new
lead compounds for known therapeutic targets. In most structure‐based drug design …

Persistent de Rham-Hodge Laplacians in the Eulerian representation

Z Su, Y Tong, GW Wei - arXiv preprint arXiv:2408.00220, 2024 - arxiv.org
Recently, topological data analysis (TDA) has become a trending topic in data science and
engineering. However, the key technique of TDA, ie, persistent homology, is defined on …

Persistent Topological Laplacians--a Survey

X Wei, GW Wei - arXiv preprint arXiv:2312.07563, 2023 - arxiv.org
Persistent topological Laplacians constitute a new class of tools in topological data analysis
(TDA), motivated by the necessity to address challenges encountered in persistent …

Predicting pKa of the carboxylic acid group in water solutions of amino acids based on molecular structures using machine learning QSPR methods

A Fazeli, M Karimzadeh - Materials Today Communications, 2023 - Elsevier
Amino acids as biomolecules are essential building blocks of proteins, which are
fundamental to life and living organisms. The pKa values of amino acid residues in proteins …

An ensemble‐based approach to estimate confidence of predicted protein–ligand binding affinity values

M Rayka, M Mirzaei… - Molecular Informatics, 2024 - Wiley Online Library
When designing a machine learning‐based scoring function, we access a limited number of
protein‐ligand complexes with experimentally determined binding affinity values …

DeepRLI: A Multi-objective Framework for Universal Protein--Ligand Interaction Prediction

H Lin, S Wang, J Zhu, Y Li, J Pei, L Lai - arXiv preprint arXiv:2401.10806, 2024 - arxiv.org
Protein (receptor)--ligand interaction prediction is a critical component in computer-aided
drug design, significantly influencing molecular docking and virtual screening processes …

[HTML][HTML] Persistent de Rham-Hodge Laplacians in Eulerian representation for manifold topological learning

Z Su, Y Tong, GW Wei - AIMS Mathematics, 2024 - aimspress.com
Recently, topological data analysis has become a trending topic in data science and
engineering. However, the key technique of topological data analysis, ie, persistent …

Enhancing Generalizability in Protein–Ligand Binding Affinity Prediction with Multimodal Contrastive Learning

D Luo, D Liu, X Qu, L Dong, B Wang - Journal of Chemical …, 2024 - ACS Publications
Improving the generalization ability of scoring functions remains a major challenge in protein–
ligand binding affinity prediction. Many machine learning methods are limited by their …

A novel functional peptide, named EQ-9 (ESETRILLQ), identified by virtual screening from regenerative cell secretome and its potential anti-aging and restoration …

W Feifei, S Wenrou, K Sining, Z Siyu, F Xiaolei… - Peptides, 2023 - Elsevier
Skin aging refers to a degenerative process that can be affected and regulated by intrinsic
and extrinsic factors. The mesenchymal stem cell secretome covers a considerable number …