From machine learning to deep learning: Advances in scoring functions for protein–ligand docking

C Shen, J Ding, Z Wang, D Cao… - Wiley Interdisciplinary …, 2020 - Wiley Online Library
learning (ML) techniques, ML-based SFs have gradually emerged as a promising alternative
for protein–ligand … Emergence of more data-hungry deep learning (DL) approaches in …

Combining docking pose rank and structure with deep learning improves protein–ligand binding mode prediction over a baseline docking approach

JA Morrone, JK Weber, T Huynh, H Luo… - Journal of chemical …, 2020 - ACS Publications
… In this work, we have developed a new set of deep learning models that take the output of
docking programs as input. Our models can be fashioned to classify activity (virtual screening) …

A deep-learning approach toward rational molecular docking protocol selection

J Jiménez-Luna, A Cuzzolin, G Bolcato, M Sturlese… - Molecules, 2020 - mdpi.com
… both select the best possible docking protocol given a protein–ligand pair and to provide
insight into which protein–ligand pairs will result in a better pose given a docking protocol. We …

Deep learning model for flexible and efficient protein-ligand docking

M Masters, AH Mahmoud, Y Wei… - … Machine Learning for Drug …, 2022 - openreview.net
… the ligand-binding process. Here we present a deep learning model for flexible protein-ligand
docking … Our method introduces a new approach for the reconstruction of ligand poses in …

Deep learning model for efficient protein–ligand docking with implicit side-chain flexibility

MR Masters, AH Mahmoud, Y Wei… - Journal of Chemical …, 2023 - ACS Publications
… essential feature of the ligand-binding process. Flexible protein–ligand docking still remains
a … , we present a deep learning (DL) model for flexible protein–ligand docking based on the …

DeepBSP—a machine learning method for accurate prediction of protein–ligand docking structures

J Bao, X He, JZH Zhang - Journal of chemical information and …, 2021 - ACS Publications
… -learning model, named DeepBSP, that can directly predict the root mean square deviation
(rmsd) of a ligand docking … Unlike the binding affinity, the rmsd between the docking poses …

Deep docking: a deep learning platform for augmentation of structure based drug discovery

F Gentile, V Agrawal, M Hsing, AT Ton, F Ban… - ACS central …, 2020 - ACS Publications
… introduce Deep Docking (DD), a novel deep learning platform that is suitable for docking
DD appears to clearly bias final sets toward high docking scores, and since active ligands

Advancing Ligand Docking through Deep Learning: Challenges and Prospects in Virtual Screening

X Zhang, C Shen, H Zhang, Y Kang… - Accounts of Chemical …, 2024 - ACS Publications
Deep learning protocols for ligand docking. (A) Predicting the protein–ligand (PL) distance
… His research focuses on the applications of deep learning in ligand docking and virtual …

DEELIG: A deep learning approach to predict protein-ligand binding affinity

A Ahmed, B Mam… - Bioinformatics and biology …, 2021 - journals.sagepub.com
Deep learning has been known to learn representations and patterns in … deep learning
to predict binding affinity of protein-nonpeptide ligand interaction without the need of a docked

Boosting docking-based virtual screening with deep learning

JC Pereira, ER Caffarena… - Journal of chemical …, 2016 - ACS Publications
… DeepVS learns abstract features that are suitable to discriminate between active ligands
deep learning to improve docking-based virtual screening. Recent works on improving docking-…