Molecular simulation for food protein–ligand interactions: A comprehensive review on principles, current applications, and emerging trends

Z Jin, Z Wei - Comprehensive Reviews in Food Science and …, 2024 - Wiley Online Library
In recent years, investigations on molecular interaction mechanisms between food proteins
and ligands have attracted much interest. The interaction mechanisms can supply much …

Virtual screening web servers: designing chemical probes and drug candidates in the cyberspace

N Singh, L Chaput, BO Villoutreix - Briefings in bioinformatics, 2021 - academic.oup.com
The interplay between life sciences and advancing technology drives a continuous cycle of
chemical data growth; these data are most often stored in open or partially open databases …

Structural biology in the clouds: the WeNMR-EOSC ecosystem

RV Honorato, PI Koukos, B Jiménez-García… - Frontiers in molecular …, 2021 - frontiersin.org
Structural biology aims at characterizing the structural and dynamic properties of biological
macromolecules at atomic details. Gaining insight into three dimensional structures of …

A candidate multi-epitope vaccine against SARS-CoV-2

T Kar, U Narsaria, S Basak, D Deb, F Castiglione… - Scientific reports, 2020 - nature.com
In the past two decades, 7 coronaviruses have infected the human population, with two
major outbreaks caused by SARS-CoV and MERS-CoV in the year 2002 and 2012 …

The lipoprotein-associated phospholipase A2 inhibitor Darapladib sensitises cancer cells to ferroptosis by remodelling lipid metabolism

M Oh, SY Jang, JY Lee, JW Kim, Y Jung, J Kim… - Nature …, 2023 - nature.com
Arachidonic and adrenic acids in the membrane play key roles in ferroptosis. Here, we
reveal that lipoprotein-associated phospholipase A2 (Lp-PLA2) controls intracellular …

Unraveling the mechanism of arbidol binding and inhibition of SARS-CoV-2: Insights from atomistic simulations

AK Padhi, A Seal, JM Khan, M Ahamed… - European journal of …, 2021 - Elsevier
The COVID-19 pandemic has spread rapidly and poses an unprecedented threat to the
global economy and human health. Broad-spectrum antivirals are currently being …

High-throughput rational design of the remdesivir binding site in the RdRp of SARS-CoV-2: implications for potential resistance

AK Padhi, R Shukla, P Saudagar, T Tripathi - Iscience, 2021 - cell.com
The use of remdesivir to treat COVID-19 will likely continue before clinical trials are
completed. Due to the lengthening pandemic and evolving nature of the virus, predicting …

Identification of fluoxetine as a direct NLRP3 inhibitor to treat atrophic macular degeneration

M Ambati, I Apicella, S Wang… - Proceedings of the …, 2021 - National Acad Sciences
The atrophic form of age-related macular degeneration (dry AMD) affects nearly 200 million
people worldwide. There is no Food and Drug Administration (FDA)-approved therapy for …

Antiviral activity of natural phenolic compounds in complex at an allosteric site of SARS-CoV-2 papain-like protease

V Srinivasan, H Brognaro, PR Prabhu… - Communications …, 2022 - nature.com
Abstract SARS-CoV-2 papain-like protease (PLpro) covers multiple functions. Beside the
cysteine-protease activity, facilitating cleavage of the viral polypeptide chain, PLpro has the …

Balancing functional tradeoffs between protein stability and ACE2 binding in the SARS-CoV-2 omicron BA. 2, BA. 2.75 and XBB lineages: dynamics-based network …

G Verkhivker, M Alshahrani, G Gupta - Viruses, 2023 - mdpi.com
Evolutionary and functional studies suggested that the emergence of the Omicron variants
can be determined by multiple fitness trade-offs including the immune escape, binding …