[HTML][HTML] Prediction of protein–ligand binding affinity from sequencing data with interpretable machine learning

HT Rube, C Rastogi, S Feng, JF Kribelbauer, A Li… - Nature …, 2022 - nature.com
Protein–ligand interactions are increasingly profiled at high throughput using affinity
selection and massively parallel sequencing. However, these assays do not provide the …

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 …

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 …

Protein-protein interaction networks and biology—what's the connection?

L Hakes, JW Pinney, DL Robertson, SC Lovell - Nature biotechnology, 2008 - nature.com
Protein-protein interaction networks and biology—what's the connection? | Nature Biotechnology
Skip to main content Thank you for visiting nature.com. You are using a browser version with …

Artificial intelligence in the prediction of protein–ligand interactions: recent advances and future directions

A Dhakal, C McKay, JJ Tanner… - Briefings in …, 2022 - academic.oup.com
New drug production, from target identification to marketing approval, takes over 12 years
and can cost around $2.6 billion. Furthermore, the COVID-19 pandemic has unveiled the …

Structural and sequence similarity makes a significant impact on machine-learning-based scoring functions for protein–ligand interactions

Y Li, J Yang - Journal of chemical information and modeling, 2017 - ACS Publications
The prediction of protein–ligand binding affinity has recently been improved remarkably by
machine-learning-based scoring functions. For example, using a set of simple descriptors …

Learning from the ligand: using ligand-based features to improve binding affinity prediction

F Boyles, CM Deane, GM Morris - Bioinformatics, 2020 - academic.oup.com
Motivation Machine learning scoring functions for protein–ligand binding affinity prediction
have been found to consistently outperform classical scoring functions. Structure-based …

[HTML][HTML] Predicting or pretending: artificial intelligence for protein-ligand interactions lack of sufficiently large and unbiased datasets

J Yang, C Shen, N Huang - Frontiers in pharmacology, 2020 - frontiersin.org
Predicting protein-ligand interactions using artificial intelligence (AI) models has attracted
great interest in recent years. However, data-driven AI models unequivocally suffer from a …

Inferring protein–protein interactions through high-throughput interaction data from diverse organisms

Y Liu, N Liu, H Zhao - Bioinformatics, 2005 - academic.oup.com
Motivation: Identifying protein–protein interactions is critical for understanding cellular
processes. Because protein domains represent binding modules and are responsible for the …

[HTML][HTML] Decoding the protein–ligand interactions using parallel graph neural networks

C Knutson, M Bontha, JA Bilbrey, N Kumar - Scientific reports, 2022 - nature.com
Protein–ligand interactions (PLIs) are essential for biochemical functionality and their
identification is crucial for estimating biophysical properties for rational therapeutic design …