ArticleChemical science2021
High-resolution mining of the SARS-CoV-2 main protease conformational space: supercomputer-driven unsupervised adaptive sampling.
Article in Chemical science, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
What it found
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The trial behind it
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Who cites it
23 citing papers in PubMed.
- Targeting RNA with small molecules using state-of-the-art methods provides highly predictive affinities of riboswitch inhibitors.Communications biology · 2025Article
- Identification of Protein Cryptic Sites via Conformational Dynamics Capturing and Water-Based Pocket Characterization in Molecular Dynamics Simulations.Journal of chemical theory and computation · 2025Article
- High-Resolution Molecular-Dynamics Simulations of the Pyruvate Kinase Muscle Isoform 1 and 2 (PKM1/2).Chemistry (Weinheim an der Bergstrasse, Germany) · 2025Article
- A Reflection on the Use of Molecular Simulation to Respond to SARS-CoV-2 Pandemic Threats.The journal of physical chemistry letters · 2025Review
- Histidine 73 methylation coordinates β-actin plasticity in response to key environmental factors.Nature communications · 2025Article
- Unveiling the mechanism of action of a novel natural dual inhibitor of SARS-CoV-2 Mpro and PLpro with molecular dynamics simulations.Natural products and bioprospecting · 2025Article
- Dynamic pre-structuration of lipid nanodomain-segregating remorin proteins.Communications biology · 2024Article
- Unveiling mutation effects on the structural dynamics of the main protease from SARS-CoV-2 with hybrid simulation methods.Journal of molecular graphics & modelling · 2023Article
- Scalable hybrid deep neural networks/polarizable potentials biomolecular simulations including long-range effects.Chemical science · 2023Article
- Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case.Wiley interdisciplinary reviews. Computational molecular science · 2022Article
- Computationally driven discovery of SARS-CoV-2 MChemical science · 2022Article
- Carboxylic submetabolome-driven signature characterization of COVID-19 asymptomatic infection.Talanta · 2022Article
- Dynamics of 5R-Tg Base Flipping in DNA Duplexes Based on Simulations─Agreement with Experiments and Beyond.Journal of chemical information and modeling · 2022Article
- A higher flexibility at the SARS-CoV-2 main protease active site compared to SARS-CoV and its potentialities for new inhibitor virtual screening targeting multi-conformers.Journal of biomolecular structure & dynamics · 2022Article
- Allosteric Binding Sites of the SARS-CoV-2 Main Protease: Potential Targets for Broad-Spectrum Anti-Coronavirus Agents.Drug design, development and therapy · 2022Review
- The dolabellane diterpenes as potential inhibitors of the SARS-CoV-2 main protease: molecular insight of the inhibitory mechanism through computational studies.RSC advances · 2021Article
- Modelling the active SARS-CoV-2 helicase complex as a basis for structure-based inhibitor design.Chemical science · 2021Article
- Precursors of Viral Proteases as Distinct Drug Targets.Viruses · 2021Review
- Integrating single-molecule spectroscopy and simulations for the study of intrinsically disordered proteins.Methods (San Diego, Calif.) · 2021Article
- Elucidation of Cryptic and Allosteric Pockets within the SARS-CoV-2 Main Protease.Journal of chemical information and modeling · 2021Article
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
We provide an unsupervised adaptive sampling strategy capable of producing μs-timescale molecular dynamics (MD) simulations of large biosystems using many-body polarizable force fields (PFFs). The global exploration problem is decomposed into a set of separate MD trajectories that can be restarted within a selective process to achieve sufficient phase-space sampling. Accurate statistical properties can be obtained through reweighting. Within this highly parallel setup, the Tinker-HP package can be powered by an arbitrary large number of GPUs on supercomputers, reducing exploration time from years to days. This approach is used to tackle the urgent modeling problem of the SARS-CoV-2 Main Protease (M
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.