ArticleThe journal of physical chemistry letters2020
The Answer Lies in the Energy: How Simple Atomistic Molecular Dynamics Simulations May Hold the Key to Epitope Prediction on the Fully Glycosylated SARS-CoV-2 Spike Protein.
Article in The journal of physical chemistry letters, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- The top 100 most cited articles on COVID-19 vaccine: a bibliometric analysis.Clinical and experimental medicine · 2023Trial
- Mass spectrometry-based mapping of conformational epitopes on SARS-CoV-2 antigens targeted by monoclonal antibodies.International journal of biological macromolecules · 2026Article
- Adaptive Disorder as the Hallmark of Nanobodies Antigen-Binding Loops.Journal of chemical information and modeling · 2026Article
- Ligand-driven modulation of chaperone-cochaperone networks shapes proteostasis outcomes.Protein science : a publication of the Protein Society · 2026Article
- Prediction of potential NS3-based T cell epitopes of hepatitis C virus by in-silico and in-vitro approach.Scientific reports · 2026Article
- N-Glycans modulate tilting of HIV-1 envelope glycoprotein.Nature communications · 2026Article
- A Reflection on the Use of Molecular Simulation to Respond to SARS-CoV-2 Pandemic Threats.The journal of physical chemistry letters · 2025Review
- Article
- Integration of Experimental and Computational Methods to Characterize Glycoproteins.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Simulation-driven design of stabilized SARS-CoV-2 spike S2 immunogens.Nature communications · 2024Article
- Review
- A Computational Biology Study on the Structure and Dynamics Determinants of Thermal Stability of the Chitosanase fromInternational journal of molecular sciences · 2023Article
- Computational Epitope Prediction and Design for Antibody Development and Detection.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Emerging COVID-19 variants and their impact on SARS-CoV-2 diagnosis, therapeutics and vaccines.Annals of medicine · 2022Review
- Computation of the Binding Energies between Human ACE2 and Spike RBDs of the Original Strain, Delta and Omicron Variants of the SARS-CoV-2: A DFT Simulation Approach.Advanced theory and simulations · 2022Article
- Molecular dynamics studies reveal structural and functional features of the SARS-CoV-2 spike protein.BioEssays : news and reviews in molecular, cellular and developmental biology · 2022Review
- SARS-CoV-2 variants and spike mutations involved in second wave of COVID-19 pandemic in India.Transboundary and emerging diseases · 2022Article
- Posttranslational modifications optimize the ability of SARS-CoV-2 spike for effective interaction with host cell receptors.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Point mutations in SARS-CoV-2 variants induce long-range dynamical perturbations in neutralizing antibodies.Chemical science · 2022Article
- Emerging of composition variations of SARS-CoV-2 spike protein and human ACE2 contribute to the level of infection:Journal of biomolecular structure & dynamics · 2022Article
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Authors and funding
9 authors.
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No grant is acknowledged in the PubMed record.
Abstract
SARS-CoV-2 is a health threat with dire socioeconomical consequences. As the crucial mediator of infection, the viral glycosylated spike protein (S) has attracted the most attention and is at the center of efforts to develop therapeutics and diagnostics. Herein, we use an original decomposition approach to identify energetically uncoupled substructures as antibody binding sites on the fully glycosylated S. Crucially, all that is required are unbiased MD simulations; no prior knowledge of binding properties or ad hoc parameter combinations is needed. Our results are validated by experimentally confirmed structures of S in complex with anti- or nanobodies. We identify poorly coupled subdomains that are poised to host (several) epitopes and potentially involved in large functional conformational transitions. Moreover, we detect two distinct behaviors for glycans: those with stronger energetic coupling are structurally relevant and protect underlying peptidic epitopes, and those with weaker coupling could themselves be prone to antibody recognition.
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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.