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 …

[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, several deep learning …

A comparative assessment of predictive accuracies of conventional and machine learning scoring functions for protein-ligand binding affinity prediction

HM Ashtawy, NR Mahapatra - IEEE/ACM transactions on …, 2014 - ieeexplore.ieee.org
Accurately predicting the binding affinities of large diverse sets of protein-ligand complexes
efficiently is a key challenge in computational biomolecular science, with applications in …

A comparative assessment of ranking accuracies of conventional and machine-learning-based scoring functions for protein-ligand binding affinity prediction

HM Ashtawy, NR Mahapatra - IEEE/ACM Transactions on …, 2012 - ieeexplore.ieee.org
Accurately predicting the binding affinities of large sets of protein-ligand complexes
efficiently is a key challenge in computational biomolecular science, with applications in …

[HTML][HTML] 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 …

Prediction of protein–ligand binding affinity via deep learning models

H Wang - Briefings in Bioinformatics, 2024 - academic.oup.com
Accurately predicting the binding affinity between proteins and ligands is crucial in drug
screening and optimization, but it is still a challenge in computer-aided drug design. The …

Improved protein–ligand binding affinity prediction with structure-based deep fusion inference

D Jones, H Kim, X Zhang, A Zemla… - Journal of chemical …, 2021 - ACS Publications
Predicting accurate protein–ligand binding affinities is an important task in drug discovery
but remains a challenge even with computationally expensive biophysics-based energy …

A machine learning approach to predicting protein–ligand binding affinity with applications to molecular docking

PJ Ballester, JBO Mitchell - Bioinformatics, 2010 - academic.oup.com
Motivation: Accurately predicting the binding affinities of large sets of diverse protein–ligand
complexes is an extremely challenging task. The scoring functions that attempt such …

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 …

Statistical and machine learning approaches to predicting protein–ligand interactions

LJ Colwell - Current opinion in structural biology, 2018 - Elsevier
Data driven computational approaches to predicting protein–ligand binding are currently
achieving unprecedented levels of accuracy on held-out test datasets. Up until now …