Learning protein-ligand binding affinity with atomic environment vectors

R Meli, A Anighoro, MJ Bodkin, GM Morris… - Journal of …, 2021 - Springer
Scoring functions for the prediction of protein-ligand binding affinity have seen renewed
interest in recent years when novel machine learning and deep learning methods started to …

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 …

[HTML][HTML] OnionNet-2: a convolutional neural network model for predicting protein-ligand binding affinity based on residue-atom contacting shells

Z Wang, L Zheng, Y Liu, Y Qu, YQ Li, M Zhao… - Frontiers in …, 2021 - frontiersin.org
One key task in virtual screening is to accurately predict the binding affinity (delta-G) of
protein-ligand complexes. Recently, deep learning (DL) has significantly increased 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 …

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 …

Extended connectivity interaction features: improving binding affinity prediction through chemical description

N Sánchez-Cruz, JL Medina-Franco, J Mestres… - …, 2021 - academic.oup.com
Motivation Machine-learning scoring functions (SFs) have been found to outperform
standard SFs for binding affinity prediction of protein–ligand complexes. A plethora of …

Binding affinity prediction by pairwise function based on neural network

F Zhu, X Zhang, JE Allen, D Jones… - Journal of chemical …, 2020 - ACS Publications
We present a new approach to estimate the binding affinity from given three-dimensional
poses of protein–ligand complexes. In this scheme, every protein–ligand atom pair makes …

[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 …

AK-score: accurate protein-ligand binding affinity prediction using an ensemble of 3D-convolutional neural networks

Y Kwon, WH Shin, J Ko, J Lee - International journal of molecular …, 2020 - mdpi.com
Accurate prediction of the binding affinity of a protein-ligand complex is essential for efficient
and successful rational drug design. Therefore, many binding affinity prediction methods …

DLSSAffinity: protein–ligand binding affinity prediction via a deep learning model

H Wang, H Liu, S Ning, C Zeng, Y Zhao - Physical Chemistry Chemical …, 2022 - pubs.rsc.org
Evaluating the protein–ligand binding affinity is a substantial part of the computer-aided drug
discovery process. Most of the proposed computational methods predict protein–ligand …