[HTML][HTML] A review on applications of computational methods in drug screening and design

X Lin, X Li, X Lin - Molecules, 2020 - mdpi.com
Drug development is one of the most significant processes in the pharmaceutical industry.
Various computational methods have dramatically reduced the time and cost of drug …

Natural product-derived phytochemicals as potential agents against coronaviruses: A review

JS Mani, JB Johnson, JC Steel, DA Broszczak… - Virus research, 2020 - Elsevier
Coronaviruses are responsible for a growing economic, social and mortality burden, as the
causative agent of diseases such as severe acute respiratory syndrome (SARS), Middle …

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 …

[HTML][HTML] PoseBusters: AI-based docking methods fail to generate physically valid poses or generalise to novel sequences

M Buttenschoen, GM Morris, CM Deane - Chemical Science, 2024 - pubs.rsc.org
The last few years have seen the development of numerous deep learning-based protein–
ligand docking methods. They offer huge promise in terms of speed and accuracy. However …

[HTML][HTML] Key topics in molecular docking for drug design

PHM Torres, ACR Sodero, P Jofily… - International journal of …, 2019 - mdpi.com
Molecular docking has been widely employed as a fast and inexpensive technique in the
past decades, both in academic and industrial settings. Although this discipline has now had …

[HTML][HTML] Molecular docking, validation, dynamics simulations, and pharmacokinetic prediction of natural compounds against the SARS-CoV-2 main-protease

C Shivanika, D Kumar, V Ragunathan… - … structure & dynamics, 2020 - ncbi.nlm.nih.gov
The study aims to evaluate the potency of two hundred natural antiviral phytocompounds
against the active site of the Severe Acquired Respiratory Syndrome-Coronavirus− 2 (SARS …

[HTML][HTML] 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 …

Bioinformatics approaches to discovering food-derived bioactive peptides: Reviews and perspectives

Z Du, J Comer, Y Li - TrAC Trends in Analytical Chemistry, 2023 - Elsevier
Food-derived bioactive peptides (FBPs) are gaining interest due to their great potential in
agricultural byproduct valorization and high-activity peptide screening. The introduction of …

Autodock vina adopts more accurate binding poses but autodock4 forms better binding affinity

NT Nguyen, TH Nguyen, TNH Pham… - Journal of Chemical …, 2019 - ACS Publications
The binding pose and affinity between a ligand and enzyme are very important pieces of
information for computer-aided drug design. In the initial stage of a drug discovery project …

Exposure to 6-PPD quinone at environmentally relevant concentrations causes abnormal locomotion behaviors and neurodegeneration in Caenorhabditis elegans

X Hua, X Feng, G Liang, J Chao… - Environmental Science & …, 2023 - ACS Publications
6-PPD quinone (6-PPDQ) can be transformed from 6-PPD through ozonation. Nevertheless,
the potential neurotoxicity of 6-PPDQ after long-term exposure and the underlying …