ArticleRoyal Society open science2022
Unbinding ligands from SARS-CoV-2 Mpro via umbrella sampling simulations.
Article in Royal Society open science, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- What Determines the Directionality of Kinesins? Studying the Anomalous Directionality of Nonclaret Disjunctional Motor Mutants.Journal of the American Chemical Society · 2026Article
- Understanding hypertrophic cardiomyopathy and its regulation by myosin drugs.Protein science : a publication of the Protein Society · 2025Article
- On the Control of Directionality of Myosin.Journal of the American Chemical Society · 2024Article
- High-throughput virtual screening of potential inhibitors of GPR52 using docking and biased sampling method for Huntington's disease therapy.Molecular diversity · 2024Article
- Energetic and structural insights behind calcium induced conformational transition in calmodulin.Proteins · 2024Article
- CHAPERONComputational and structural biotechnology journal · 2023Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The umbrella sampling (US) simulation is demonstrated to be an efficient approach for determining the unbinding pathway and binding affinity to the SARS-CoV-2 Mpro of small molecule inhibitors. The accuracy of US is in the same range as the linear interaction energy (LIE) and fast pulling of ligand (FPL) methods. In detail, the correlation coefficient between US and experiments does not differ from FPL and is slightly smaller than LIE. The root mean square error of US simulations is smaller than that of LIE. Moreover, US is better than FPL and poorer than LIE in classifying SARS-CoV-2 Mpro inhibitors owing to the reciever operating characteristic-area under the curve analysis. Furthermore, the US simulations also provide detailed insights on unbinding pathways of ligands from the binding cleft of SARS-CoV-2 Mpro. The residues
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