Relative binding free energy calculations in drug discovery: recent advances and practical considerations

Z Cournia, B Allen, W Sherman - Journal of chemical information …, 2017 - ACS Publications
Accurate in silico prediction of protein–ligand binding affinities has been a primary objective
of structure-based drug design for decades due to the putative value it would bring to the …

An overview of scoring functions used for protein–ligand interactions in molecular docking

J Li, A Fu, L Zhang - Interdisciplinary Sciences: Computational Life …, 2019 - Springer
Currently, molecular docking is becoming a key tool in drug discovery and molecular
modeling applications. The reliability of molecular docking depends on the accuracy of the …

Structure of a signaling cannabinoid receptor 1-G protein complex

KK Kumar, M Shalev-Benami, MJ Robertson, H Hu… - Cell, 2019 - cell.com
Cannabis elicits its mood-enhancing and analgesic effects through the cannabinoid receptor
1 (CB1), a G protein-coupled receptor (GPCR) that signals primarily through the adenylyl …

Role of molecular dynamics and related methods in drug discovery

M De Vivo, M Masetti, G Bottegoni… - Journal of medicinal …, 2016 - ACS Publications
Molecular dynamics (MD) and related methods are close to becoming routine computational
tools for drug discovery. Their main advantage is in explicitly treating structural flexibility and …

G-protein activation by a metabotropic glutamate receptor

AB Seven, X Barros-Álvarez, M de Lapeyrière… - Nature, 2021 - nature.com
Family C G-protein-coupled receptors (GPCRs) operate as obligate dimers with extracellular
domains that recognize small ligands, leading to G-protein activation on the transmembrane …

Alchemical binding free energy calculations in AMBER20: Advances and best practices for drug discovery

TS Lee, BK Allen, TJ Giese, Z Guo, P Li… - Journal of Chemical …, 2020 - ACS Publications
Predicting protein–ligand binding affinities and the associated thermodynamics of
biomolecular recognition is a primary objective of structure-based drug design. Alchemical …

[HTML][HTML] A guide to in silico drug design

Y Chang, BA Hawkins, JJ Du, PW Groundwater… - Pharmaceutics, 2023 - mdpi.com
The drug discovery process is a rocky path that is full of challenges, with the result that very
few candidates progress from hit compound to a commercially available product, often due …

Structure-based virtual screening for drug discovery: principles, applications and recent advances

E Lionta, G Spyrou, DK Vassilatis… - Current topics in …, 2014 - ingentaconnect.com
Structure-based drug discovery (SBDD) is becoming an essential tool in assisting fast and
cost-efficient lead discovery and optimization. The application of rational, structure-based …

Docking screens for novel ligands conferring new biology: Miniperspective

JJ Irwin, BK Shoichet - Journal of medicinal chemistry, 2016 - ACS Publications
It is now plausible to dock libraries of 10 million molecules against targets over several days
or weeks. When the molecules screened are commercially available, they may be rapidly …

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 …