An analysis of proteochemometric and conformal prediction machine learning protein-ligand binding affinity models

C Parks, Z Gaieb, RE Amaro - Frontiers in molecular biosciences, 2020 - frontiersin.org
Protein-ligand binding affinity is a key pharmacodynamic endpoint in drug discovery. Sole
reliance on experimental design, make, and test cycles is costly and time consuming …

A versatile deep learning-based protein-ligand interaction prediction model for accurate binding affinity scoring and virtual screening

S Moon, SY Hwang, J Lim, WY Kim - arXiv preprint arXiv:2307.01066, 2023 - arxiv.org
Protein--ligand interaction (PLI) prediction is critical in drug discovery, aiding the
identification and enhancement of molecules that effectively bind to target proteins. Despite …

Latent biases in machine learning models for predicting binding affinities using popular data sets

GC Kanakala, R Aggarwal, D Nayar… - ACS omega, 2023 - ACS Publications
Drug design involves the process of identifying and designing molecules that bind well to a
given receptor. A vital computational component of this process is the protein–ligand …

PIGNet2: a versatile deep learning-based protein–ligand interaction prediction model for binding affinity scoring and virtual screening

S Moon, SY Hwang, J Lim, WY Kim - Digital Discovery, 2024 - pubs.rsc.org
Prediction of protein–ligand interactions (PLI) plays a crucial role in drug discovery as it
guides the identification and optimization of molecules that effectively bind to target proteins …

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 …

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 …

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 …

Comparison of scaling methods to obtain calibrated probabilities of activity for protein–ligand predictions

LH Mervin, AM Afzal, O Engkvist… - Journal of Chemical …, 2020 - ACS Publications
In the context of bioactivity prediction, the question of how to calibrate a score produced by a
machine learning method into a probability of binding to a protein target is not yet …

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 …