A practical guide to machine-learning scoring for structure-based virtual screening

VK Tran-Nguyen, M Junaid, S Simeon, PJ Ballester - Nature Protocols, 2023 - nature.com
Abstract Structure-based virtual screening (SBVS) via docking has been used to discover
active molecules for a range of therapeutic targets. Chemical and protein data sets that …

[HTML][HTML] Scoring functions for protein-ligand binding affinity prediction using structure-based deep learning: a review

R Meli, GM Morris, PC Biggin - Frontiers in bioinformatics, 2022 - frontiersin.org
The rapid and accurate in silico prediction of protein-ligand binding free energies or binding
affinities has the potential to transform drug discovery. In recent years, there has been a …

[HTML][HTML] Preparation and evaluation of chitosan/PVA based hydrogel films loaded with honey for wound healing application

H Chopra, S Bibi, S Kumar, MS Khan, P Kumar, I Singh - Gels, 2022 - mdpi.com
In the present study, chitosan/polyvinyl alcohol (PVA)-based honey hydrogel films were
developed for potential wound healing application. The hydrogel films were developed by a …

Relation: A deep generative model for structure-based de novo drug design

M Wang, CY Hsieh, J Wang, D Wang… - Journal of Medicinal …, 2022 - ACS Publications
Deep learning (DL)-based de novo molecular design has recently gained considerable
traction. Many DL-based generative models have been successfully developed to design …

[HTML][HTML] A generalized protein–ligand scoring framework with balanced scoring, docking, ranking and screening powers

C Shen, X Zhang, CY Hsieh, Y Deng, D Wang, L Xu… - Chemical …, 2023 - pubs.rsc.org
Applying machine learning algorithms to protein–ligand scoring functions has aroused
widespread attention in recent years due to the high predictive accuracy and affordable …

Conserved sites and recognition mechanisms of T1R1 and T2R14 receptors revealed by ensemble docking and molecular descriptors and fingerprints combined with …

Z Cui, N Zhang, T Zhou, X Zhou, H Meng… - Journal of Agricultural …, 2023 - ACS Publications
Taste peptides, as an important component of protein-rich foodstuffs, potentiate the nutrition
and taste of food. Thereinto, umami-and bitter-taste peptides have been ex tensively …

Can molecular dynamics simulations improve predictions of protein-ligand binding affinity with machine learning?

S Gu, C Shen, J Yu, H Zhao, H Liu, L Liu… - Briefings in …, 2023 - academic.oup.com
Binding affinity prediction largely determines the discovery efficiency of lead compounds in
drug discovery. Recently, machine learning (ML)-based approaches have attracted much …

[HTML][HTML] TB-IECS: an accurate machine learning-based scoring function for virtual screening

X Zhang, C Shen, D Jiang, J Zhang, Q Ye, L Xu… - Journal of …, 2023 - Springer
Abstract Machine learning-based scoring functions (MLSFs) have shown potential for
improving virtual screening capabilities over classical scoring functions (SFs). Due to the …

Machine Learning for Sequence and Structure-Based Protein–Ligand Interaction Prediction

Y Zhang, S Li, K Meng, S Sun - Journal of Chemical Information …, 2024 - ACS Publications
Developing new drugs is too expensive and time-consuming. Accurately predicting the
interaction between drugs and targets will likely change how the drug is discovered …

The experimentalist's guide to machine learning for small molecule design

SE Lindley, Y Lu, D Shukla - ACS Applied Bio Materials, 2023 - ACS Publications
Initially part of the field of artificial intelligence, machine learning (ML) has become a
booming research area since branching out into its own field in the 1990s. After three …