Three-dimensional convolutional neural networks and a cross-docked data set for structure-based drug design

PG Francoeur, T Masuda, J Sunseri, A Jia… - Journal of chemical …, 2020 - ACS Publications
One of the main challenges in drug discovery is predicting protein–ligand binding affinity.
Recently, machine learning approaches have made substantial progress on this task …

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 …

Fabind: Fast and accurate protein-ligand binding

Q Pei, K Gao, L Wu, J Zhu, Y Xia… - Advances in …, 2024 - proceedings.neurips.cc
Modeling the interaction between proteins and ligands and accurately predicting their
binding structures is a critical yet challenging task in drug discovery. Recent advancements …

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 …

Protein–ligand scoring with convolutional neural networks

M Ragoza, J Hochuli, E Idrobo, J Sunseri… - Journal of chemical …, 2017 - ACS Publications
Computational approaches to drug discovery can reduce the time and cost associated with
experimental assays and enable the screening of novel chemotypes. Structure-based drug …

Deep learning in drug design: protein-ligand binding affinity prediction

MA Rezaei, Y Li, D Wu, X Li, C Li - IEEE/ACM transactions on …, 2020 - ieeexplore.ieee.org
Computational drug design relies on the calculation of binding strength between two
biological counterparts especially a chemical compound, ie, a ligand, and a protein …

From proteins to ligands: decoding deep learning methods for binding affinity prediction

R Gorantla, A Kubincova, AY Weiße… - Journal of Chemical …, 2023 - ACS Publications
Accurate in silico prediction of protein–ligand binding affinity is important in the early stages
of drug discovery. Deep learning-based methods exist but have yet to overtake more …

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
We present a simple, modular graph-based convolutional neural network that takes
structural information from protein–ligand complexes as input to generate models for activity …

Tankbind: Trigonometry-aware neural networks for drug-protein binding structure prediction

W Lu, Q Wu, J Zhang, J Rao, C Li… - Advances in neural …, 2022 - proceedings.neurips.cc
Illuminating interactions between proteins and small drug molecules is a long-standing
challenge in the field of drug discovery. Despite the importance of understanding these …

Predicting protein–ligand docking structure with graph neural network

H Jiang, J Wang, W Cong, Y Huang… - Journal of chemical …, 2022 - ACS Publications
Modern day drug discovery is extremely expensive and time consuming. Although
computational approaches help accelerate and decrease the cost of drug discovery, existing …