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 …

Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases

AS Rifaioglu, H Atas, MJ Martin… - Briefings in …, 2019 - academic.oup.com
The identification of interactions between drugs/compounds and their targets is crucial for
the development of new drugs. In vitro screening experiments (ie bioassays) are frequently …

DeepSite: protein-binding site predictor using 3D-convolutional neural networks

J Jiménez, S Doerr, G Martínez-Rosell, AS Rose… - …, 2017 - academic.oup.com
Motivation An important step in structure-based drug design consists in the prediction of
druggable binding sites. Several algorithms for detecting binding cavities, those likely to …

Computational methods in drug discovery

G Sliwoski, S Kothiwale, J Meiler, EW Lowe - Pharmacological reviews, 2014 - ASPET
Computer-aided drug discovery/design methods have played a major role in the
development of therapeutically important small molecules for over three decades. These …

Molecular recognition in chemical and biological systems

E Persch, O Dumele, F Diederich - … Chemie International Edition, 2015 - Wiley Online Library
Abstract Structure‐based ligand design in medicinal chemistry and crop protection relies on
the identification and quantification of weak noncovalent interactions and understanding the …

Predicting drug metabolism: experiment and/or computation?

J Kirchmair, AH Göller, D Lang, J Kunze… - Nature reviews Drug …, 2015 - nature.com
Drug metabolism can produce metabolites with physicochemical and pharmacological
properties that differ substantially from those of the parent drug, and consequently has …

Binding site detection remastered: enabling fast, robust, and reliable binding site detection and descriptor calculation with DoGSite3

J Graef, C Ehrt, M Rarey - Journal of Chemical Information and …, 2023 - ACS Publications
Binding site prediction on protein structures is a crucial step in early phase drug discovery
whenever experimental or predicted structure models are involved. DoGSite belongs to the …

Fpocket: an open source platform for ligand pocket detection

V Le Guilloux, P Schmidtke, P Tuffery - BMC bioinformatics, 2009 - Springer
Background Virtual screening methods start to be well established as effective approaches
to identify hits, candidates and leads for drug discovery research. Among those, structure …

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 …

Combining global and local measures for structure-based druggability predictions

A Volkamer, D Kuhn, T Grombacher… - Journal of chemical …, 2012 - ACS Publications
Predicting druggability and prioritizing certain disease modifying targets for the drug
development process is of high practical relevance in pharmaceutical research …