Structure-based virtual screening for ligands of G protein–coupled receptors: what can molecular docking do for you?

F Ballante, AJ Kooistra, S Kampen, C de Graaf… - Pharmacological …, 2021 - ASPET
G protein–coupled receptors (GPCRs) constitute the largest family of membrane proteins in
the human genome and are important therapeutic targets. During the last decade, the …

The art and science of molecular docking

JM Paggi, A Pandit, RO Dror - Annual Review of Biochemistry, 2024 - annualreviews.org
Molecular docking has become an essential part of a structural biologist's and medicinal
chemist's toolkits. Given a chemical compound and the three-dimensional structure of a …

Efficient exploration of chemical space with docking and deep learning

Y Yang, K Yao, MP Repasky, K Leswing… - Journal of Chemical …, 2021 - ACS Publications
With the advent of make-on-demand commercial libraries, the number of purchasable
compounds available for virtual screening and assay has grown explosively in recent years …

Docking for EP4R antagonists active against inflammatory pain

S Gahbauer, C DeLeon, JM Braz, V Craik… - Nature …, 2023 - nature.com
The lipid prostaglandin E2 (PGE2) mediates inflammatory pain by activating G protein-
coupled receptors, including the prostaglandin E2 receptor 4 (EP4R). Nonsteroidal anti …

The impact of supervised learning methods in ultralarge high-throughput docking

CN Cavasotto, JI Di Filippo - Journal of Chemical Information and …, 2023 - ACS Publications
Structure-based virtual screening methods are, nowadays, one of the key pillars of
computational drug discovery. In recent years, a series of studies have reported docking …

[HTML][HTML] Structure-based discovery of conformationally selective inhibitors of the serotonin transporter

I Singh, A Seth, CB Billesbølle, J Braz, RM Rodriguiz… - Cell, 2023 - cell.com
The serotonin transporter (SERT) removes synaptic serotonin and is the target of anti-
depressant drugs. SERT adopts three conformations: outward-open, occluded, and inward …

Regression-based active learning for accessible acceleration of ultra-large library docking

E Marin, M Kovaleva, M Kadukova… - Journal of chemical …, 2023 - ACS Publications
Structure-based drug discovery is a process for both hit finding and optimization that relies
on a validated three-dimensional model of a target biomolecule, used to rationalize the …

Large-scale docking in the cloud

BI Tingle, JJ Irwin - Journal of Chemical Information and Modeling, 2023 - ACS Publications
Molecular docking is a pragmatic approach to exploit protein structures for new ligand
discovery, but the growing size of available chemical space is increasingly challenging to …

Targeting in silico GPCR conformations with ultra-large library screening for hit discovery

D Sala, H Batebi, K Ledwitch, PW Hildebrand… - Trends in …, 2023 - cell.com
The use of deep machine learning (ML) in protein structure prediction has made it possible
to easily access a large number of annotated conformations that can potentially compensate …

DockOpt: A tool for automatic optimization of docking models

IS Knight, O Mailhot, KG Tang… - Journal of Chemical …, 2024 - ACS Publications
Molecular docking is a widely used technique for leveraging protein structure for ligand
discovery, but it remains difficult to utilize due to limitations that have not been adequately …