ArticleeLife2019
Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'.
Article in eLife, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
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- Structural mechanisms behind the neutralisation of long-chain α-neurotoxins by broadly neutralising VCommunications chemistry · 2025Article
- Orally delivered toxin-binding protein protects against diarrhoea in a murine cholera model.Nature communications · 2025Article
- A single mutation in dairy cow-associated H5N1 viruses increases receptor binding breadth.Nature communications · 2024Article
- Defining the cross-reactivity between peanut allergens Ara h 2 and Ara h 6 using monoclonal antibodies.Clinical and experimental immunology · 2024Article
- The Role of Force Fields and Water Models in Protein Folding and Unfolding Dynamics.Journal of chemical theory and computation · 2024Article
- Guidelines for Free-Energy Calculations Involving Charge Changes.Journal of chemical theory and computation · 2024Article
- Phage display assisted discovery of a pH-dependent anti-α-cobratoxin antibody from a natural variable domain library.Protein science : a publication of the Protein Society · 2023Article
- Structural Investigation of DHICA Eumelanin Using Density Functional Theory and Classical Molecular Dynamics Simulations.Molecules (Basel, Switzerland) · 2022Article
- Implementation of Telescoping Boxes in Adaptive Steered Molecular Dynamics.Journal of chemical theory and computation · 2022Article
- Nanobody Paratope Ensembles in Solution Characterized by MD Simulations and NMR.International journal of molecular sciences · 2022Article
- Dynamics of camel and human hemoglobin revealed by molecular simulations.Scientific reports · 2022Article
- Comparing Antibody Interfaces to Inform Rational Design of New Antibody Formats.Frontiers in molecular biosciences · 2022Article
- The influence of antibody humanization on shark variable domain (VNAR) binding site ensembles.Frontiers in immunology · 2022Article
- Ensembles Are Required to Handle Aleatoric and Parametric Uncertainty in Molecular Dynamics Simulation.Journal of chemical theory and computation · 2021Article
- Article
- Uncertainty quantification in classical molecular dynamics.Philosophical transactions. Series A, Mathematical, physical, and engineering sciences · 2021Article
- Accurate absolute free energies for ligand-protein binding based on non-equilibrium approaches.Communications chemistry · 2021Article
- Biomolecular Modeling and Simulation: A Prospering Multidisciplinary Field.Annual review of biophysics · 2021Article
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2 authors.
Funding
Abstract
A recent molecular dynamics investigation into the stability of hemoglobin concluded that the unliganded protein is only stable in the T state when a solvent box is used in the simulations that is ten times larger than what is usually employed (El Hage et al., 2018). Here, we express three main concerns about that study. In addition, we find that with an order of magnitude more statistics, the reported box size dependence is not reproducible. Overall, no significant effects on the kinetics or thermodynamics of conformational transitions were observed.
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Registered trials
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