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
Molecule docking has been regarded as a routine tool for drug discovery, but its accuracy
highly depends on the reliability of scoring functions (SFs). With the rapid development of …

Can machine learning consistently improve the scoring power of classical scoring functions? Insights into the role of machine learning in scoring functions

C Shen, Y Hu, Z Wang, X Zhang, H Zhong… - Briefings in …, 2021 - academic.oup.com
How to accurately estimate protein–ligand binding affinity remains a key challenge in
computer-aided drug design (CADD). In many cases, it has been shown that the binding …

[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 …

Improving protein–ligand docking and screening accuracies by incorporating a scoring function correction term

L Zheng, J Meng, K Jiang, H Lan, Z Wang… - Briefings in …, 2022 - academic.oup.com
Scoring functions are important components in molecular docking for structure-based drug
discovery. Traditional scoring functions, generally empirical-or force field-based, are robust …

Machine-learning methods for ligand–protein molecular docking

K Crampon, A Giorkallos, M Deldossi, S Baud… - Drug discovery today, 2022 - Elsevier
Artificial intelligence (AI) is often presented as a new Industrial Revolution. Many domains
use AI, including molecular simulation for drug discovery. In this review, we provide an …

Task-specific scoring functions for predicting ligand binding poses and affinity and for screening enrichment

HM Ashtawy, NR Mahapatra - Journal of chemical information and …, 2018 - ACS Publications
Molecular docking, scoring, and virtual screening play an increasingly important role in
computer-aided drug discovery. Scoring functions (SFs) are typically employed to predict the …

[HTML][HTML] Substituting random forest for multiple linear regression improves binding affinity prediction of scoring functions: Cyscore as a case study

H Li, KS Leung, MH Wong, PJ Ballester - BMC bioinformatics, 2014 - Springer
Background State-of-the-art protein-ligand docking methods are generally limited by the
traditionally low accuracy of their scoring functions, which are used to predict binding affinity …

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
In recent years, machine-learning-based scoring functions have significantly improved the
scoring power. However, many of these methods do not perform well in distinguishing the …

Machine learning in computational docking

MA Khamis, W Gomaa, WF Ahmed - Artificial intelligence in medicine, 2015 - Elsevier
Objective The objective of this paper is to highlight the state-of-the-art machine learning (ML)
techniques in computational docking. The use of smart computational methods in the life …

A fully differentiable ligand pose optimization framework guided by deep learning and a traditional scoring function

Z Wang, L Zheng, S Wang, M Lin, Z Wang… - Briefings in …, 2023 - academic.oup.com
The recently reported machine learning-or deep learning-based scoring functions (SFs)
have shown exciting performance in predicting protein–ligand binding affinities with fruitful …