Molecular docking and structure-based drug design strategies

LG Ferreira, RN Dos Santos, G Oliva, AD Andricopulo - Molecules, 2015 - mdpi.com
Pharmaceutical research has successfully incorporated a wealth of molecular modeling
methods, within a variety of drug discovery programs, to study complex biological and …

Empirical scoring functions for structure-based virtual screening: applications, critical aspects, and challenges

IA Guedes, FSS Pereira, LE Dardenne - Frontiers in pharmacology, 2018 - frontiersin.org
Structure-based virtual screening (VS) is a widely used approach that employs the
knowledge of the three-dimensional structure of the target of interest in the design of new …

AutoDock Vina 1.2. 0: New docking methods, expanded force field, and python bindings

J Eberhardt, D Santos-Martins… - Journal of chemical …, 2021 - ACS Publications
AutoDock Vina is arguably one of the fastest and most widely used open-source programs
for molecular docking. However, compared to other programs in the AutoDock Suite, it lacks …

An activity-guided map of electrophile-cysteine interactions in primary human T cells

EV Vinogradova, X Zhang, D Remillard, DC Lazar… - Cell, 2020 - cell.com
Electrophilic compounds originating from nature or chemical synthesis have profound effects
on immune cells. These compounds are thought to act by cysteine modification to alter the …

Structural insight into molecular mechanism of poly (ethylene terephthalate) degradation

S Joo, IJ Cho, H Seo, HF Son, HY Sagong… - Nature …, 2018 - nature.com
Plastics, including poly (ethylene terephthalate)(PET), possess many desirable
characteristics and thus are widely used in daily life. However, non-biodegradability, once …

Computational protein–ligand docking and virtual drug screening with the AutoDock suite

S Forli, R Huey, ME Pique, MF Sanner, DS Goodsell… - Nature protocols, 2016 - nature.com
Computational docking can be used to predict bound conformations and free energies of
binding for small-molecule ligands to macromolecular targets. Docking is widely used for the …

Structural basis for the tethered peptide activation of adhesion GPCRs

YQ **, P **ao, F Yang, RJ Zhao, SC Guo, X Yan… - Nature, 2022 - nature.com
Adhesion G-protein-coupled receptors (aGPCRs) are important for organogenesis,
neurodevelopment, reproduction and other processes,,,,–. Many aGPCRs are activated by a …

Accelerating AutoDock4 with GPUs and Gradient-Based Local Search

D Santos-Martins, L Solis-Vasquez… - Journal of chemical …, 2021 - ACS Publications
AutoDock4 is a widely used program for docking small molecules to macromolecular targets.
It describes ligand–receptor interactions using a physics-inspired scoring function that has …

Structure, function and pharmacology of human itch receptor complexes

F Yang, L Guo, Y Li, G Wang, J Wang, C Zhang… - Nature, 2021 - nature.com
In the clades of animals that diverged from the bony fish, a group of Mas-related G-protein-
coupled receptors (MRGPRs) evolved that have an active role in itch and allergic signals …

Covalent inhibitors design and discovery

S De Cesco, J Kurian, C Dufresne… - European Journal of …, 2017 - Elsevier
In the history of therapeutics, covalent drugs occupy a very distinct category. While
representing a significant fraction of the drugs on the market, very few have been …