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] Protein–ligand docking in the machine-learning era

C Yang, EA Chen, Y Zhang - Molecules, 2022 - mdpi.com
Molecular docking plays a significant role in early-stage drug discovery, from structure-
based virtual screening (VS) to hit-to-lead optimization, and its capability and predictive …

On the frustration to predict binding affinities from protein–ligand structures with deep neural networks

M Volkov, JA Turk, N Drizard, N Martin… - Journal of medicinal …, 2022 - ACS Publications
Accurate prediction of binding affinities from protein–ligand atomic coordinates remains a
major challenge in early stages of drug discovery. Using modular message passing graph …

Multiscale topology-enabled structure-to-sequence transformer for protein–ligand interaction predictions

D Chen, J Liu, GW Wei - Nature Machine Intelligence, 2024 - nature.com
Despite the success of pretrained natural language processing (NLP) models in various
fields, their application in computational biology has been hindered by their reliance on …

Planet: a multi-objective graph neural network model for protein–ligand binding affinity prediction

X Zhang, H Gao, H Wang, Z Chen… - Journal of Chemical …, 2023 - ACS Publications
Predicting protein–ligand binding affinity is a central issue in drug design. Various deep
learning models have been published in recent years, where many of them rely on 3D …

Integrated molecular modeling and machine learning for drug design

S **a, E Chen, Y Zhang - Journal of chemical theory and …, 2023 - ACS Publications
Modern therapeutic development often involves several stages that are interconnected, and
multiple iterations are usually required to bring a new drug to the market. Computational …

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 …

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 …

Delta machine learning to improve scoring-ranking-screening performances of protein–ligand scoring functions

C Yang, Y Zhang - Journal of chemical information and modeling, 2022 - ACS Publications
Protein–ligand scoring functions are widely used in structure-based drug design for fast
evaluation of protein–ligand interactions, and it is of strong interest to develop scoring …

Different applications of machine learning approaches in materials science and engineering: Comprehensive review

Y Cao, AT Nakhjiri, M Ghadiri - Engineering Applications of Artificial …, 2024 - Elsevier
Over the last decades, considerable advancements in artificial intelligence (AI) approaches
have eventuated in their extensive applications in all scientific scopes such as materials …