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 …

Artificial intelligence in virtual screening: Models versus experiments

NA Murugan, GR Priya, GN Sastry, S Markidis - Drug Discovery Today, 2022 - Elsevier
A typical drug discovery project involves identifying active compounds with significant
binding potential for selected disease-specific targets. Experimental high-throughput …

On the frustration to predict binding affinities from protein–ligand structures with deep neural networks

M Volkov, JA Turk, N Drizard, N Martin… - Journal of medicinal …, 2022 - ACS Publications
Accurate prediction of binding affinities from protein–ligand atomic coordinates remains a
major challenge in early stages of drug discovery. Using modular message passing graph …

[HTML][HTML] A brief review of protein–ligand interaction prediction

L Zhao, Y Zhu, J Wang, N Wen, C Wang… - Computational and …, 2022 - Elsevier
The task of identifying protein–ligand interactions (PLIs) plays a prominent role in the field of
drug discovery. However, it is infeasible to identify potential PLIs via costly and laborious in …

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 …

Deepbindgcn: Integrating molecular vector representation with graph convolutional neural networks for protein–ligand interaction prediction

H Zhang, KM Saravanan, JZH Zhang - Molecules, 2023 - mdpi.com
The core of large-scale drug virtual screening is to select the binders accurately and
efficiently with high affinity from large libraries of small molecules in which non-binders are …

Improving protein–ligand interaction modeling with cryo-em data, templates, and deep learning in 2021 ligand model challenge

N Giri, J Cheng - Biomolecules, 2023 - mdpi.com
Elucidating protein–ligand interaction is crucial for studying the function of proteins and
compounds in an organism and critical for drug discovery and design. The problem of …

Recent advancements in computational drug design algorithms through machine learning and optimization

S Choudhuri, M Yendluri, S Poddar, A Li… - Kinases and …, 2023 - mdpi.com
The goal of drug discovery is to uncover new molecules with specific chemical properties
that can be used to cure diseases. With the accessibility of machine learning techniques, the …

Sunsetting binding MOAD with its last data update and the addition of 3D-ligand polypharmacology tools

S Wagle, RD Smith, AJ Dominic III, D DasGupta… - Scientific Reports, 2023 - nature.com
Binding MOAD is a database of protein–ligand complexes and their affinities with many
structured relationships across the dataset. The project has been in development for over 20 …

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 …