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 …

Binding affinity prediction for protein–ligand complex using deep attention mechanism based on intermolecular interactions

S Seo, J Choi, S Park, J Ahn - BMC bioinformatics, 2021 - Springer
Background Accurate prediction of protein–ligand binding affinity is important for lowering
the overall cost of drug discovery in structure-based drug design. For accurate predictions …

Computationally predicting binding affinity in protein–ligand complexes: free energy-based simulations and machine learning-based scoring functions

DD Wang, M Zhu, H Yan - Briefings in bioinformatics, 2021 - academic.oup.com
Accurately predicting protein–ligand binding affinities can substantially facilitate the drug
discovery process, but it remains as a difficult problem. To tackle the challenge, many …

Effects of data quality and quantity on deep learning for protein-ligand binding affinity prediction

FJ Fan, Y Shi - Bioorganic & Medicinal Chemistry, 2022 - Elsevier
Prediction of protein-ligand binding affinities is crucial for computational drug discovery. A
number of deep learning approaches have been developed in recent years to improve the …

BgN-Score and BsN-Score: Bagging and boosting based ensemble neural networks scoring functions for accurate binding affinity prediction of protein-ligand …

HM Ashtawy, NR Mahapatra - BMC bioinformatics, 2015 - Springer
Background Accurately predicting the binding affinities of large sets of protein-ligand
complexes is a key challenge in computational biomolecular science, with applications in …

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

A Ahmed, B Mam… - Bioinformatics and biology …, 2021 - journals.sagepub.com
Protein-ligand binding prediction has extensive biological significance. Binding affinity helps
in understanding the degree of protein-ligand interactions and is a useful measure in drug …

CAPLA: improved prediction of protein–ligand binding affinity by a deep learning approach based on a cross-attention mechanism

Z Jin, T Wu, T Chen, D Pan, X Wang, J Xie… - …, 2023 - academic.oup.com
Motivation Accurate and rapid prediction of protein–ligand binding affinity is a great
challenge currently encountered in drug discovery. Recent advances have manifested a …

Supervised machine learning methods applied to predict ligand-binding affinity

GS Heck, VO Pintro, RR Pereira… - Current medicinal …, 2017 - ingentaconnect.com
Background: Calculation of ligand-binding affinity is an open problem in computational
medicinal chemistry. The ability to computationally predict affinities has a beneficial impact …

KDEEP: Protein–Ligand Absolute Binding Affinity Prediction via 3D-Convolutional Neural Networks

J Jiménez, M Skalic, G Martinez-Rosell… - Journal of chemical …, 2018 - ACS Publications
Accurately predicting protein–ligand binding affinities is an important problem in
computational chemistry since it can substantially accelerate drug discovery for virtual …

Hac-net: A hybrid attention-based convolutional neural network for highly accurate protein–ligand binding affinity prediction

GW Kyro, RI Brent, VS Batista - Journal of Chemical Information …, 2023 - ACS Publications
Applying deep learning concepts from image detection and graph theory has greatly
advanced protein–ligand binding affinity prediction, a challenge with enormous ramifications …