MEDIATE-Molecular DockIng at homE: Turning collaborative simulations into therapeutic solutions

G Vistoli, C Manelfi, C Talarico, A Fava… - Expert Opinion on …, 2023 - Taylor & Francis
Introduction Collaborative computing has attracted great interest, enabling researchers
worldwide to come together and work seamlessly. Its relevance has never been so apparent …

Quercetin improves pancreatic cancer chemo‐sensitivity by regulating oxidative‐inflammatory networks

Y Hu, R Li, J Jin, Y Wang, R Ma - Journal of Food Biochemistry, 2022 - Wiley Online Library
Chemotherapy is the main method for controlling pancreatic cancer metastasis but the
prevalent chemotherapy resistance limits its utilization. The response of oxidation and …

SwissDock 2024: major enhancements for small-molecule docking with Attracting Cavities and AutoDock Vina

M Bugnon, UF Röhrig, M Goullieux… - Nucleic Acids …, 2024 - academic.oup.com
Drug discovery aims to identify potential therapeutic compounds capable of modulating the
activity of specific biological targets. Molecular docking can efficiently support this process …

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 …

Redocking the PDB

F Flachsenberg, C Ehrt, T Gutermuth… - Journal of Chemical …, 2023 - ACS Publications
Molecular docking is a standard technique in structure-based drug design (SBDD). It aims to
predict the 3D structure of a small molecule in the binding site of a receptor (often a protein) …

The efficacy of Paxlovid against COVID-19 is the result of the tight molecular docking between Mpro and antiviral drugs (nirmatrelvir and ritonavir)

AA Dawood - Advances in Medical Sciences, 2023 - Elsevier
Purpose Currently, a number of medications for coronavirus disease 2019 (COVID-19)
treatment are tested in clinical trials; however, credible clinical studies are becoming …

Dissection of the catalytic mechanisms of transmembrane terpene cyclases involved in fungal meroterpenoid biosynthesis

J Tang, Y Matsuda - Angewandte Chemie, 2023 - Wiley Online Library
Pyr4‐family terpene cyclases are noncanonical transmembrane terpene cyclases involved
in the biosynthesis of microbial meroterpenoids and catalyze diverse cyclization reactions …

Computer-aided drug design: an update

W Yu, DJ Weber, AD MacKerell Jr - Antibiotics: Methods and Protocols, 2022 - Springer
Computer-aided drug design (CADD) approaches are playing an increasingly important role
in understanding the fundamentals of ligand-receptor interactions and helping medicinal …

MolModa: accessible and secure molecular docking in a web browser

Y Kochnev, M Ahmed, AM Maldonado… - Nucleic Acids …, 2024 - academic.oup.com
Molecular docking advances early-stage drug discovery by predicting the geometries and
affinities of small-molecule compounds bound to drug-target receptors, predictions that …

ReverseDock: a web server for blind docking of a single ligand to multiple protein targets using AutoDock Vina

F Krause, K Voigt, B Di Ventura… - Frontiers in Molecular …, 2023 - frontiersin.org
Several platforms exist to perform molecular docking to computationally predict binders to a
specific protein target from a library of ligands. The reverse, that is, docking a single ligand to …