ArticleeLife2019
Response to 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 8 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
8 citing papers in PubMed.
- Evaluating sheep hemoglobins with MD simulations as an animal model for sickle cell disease.Scientific reports · 2024Article
- Implementation of Telescoping Boxes in Adaptive Steered Molecular Dynamics.Journal of chemical theory and computation · 2022Article
- Dynamics of camel and human hemoglobin revealed by molecular simulations.Scientific reports · 2022Article
- Ensembles Are Required to Handle Aleatoric and Parametric Uncertainty in Molecular Dynamics Simulation.Journal of chemical theory and computation · 2021Article
- Uncertainty quantification in classical molecular dynamics.Philosophical transactions. Series A, Mathematical, physical, and engineering sciences · 2021Article
- Biomolecular Modeling and Simulation: A Prospering Multidisciplinary Field.Annual review of biophysics · 2021Article
- Rapid, accurate, precise and reproducible ligand-protein binding free energy prediction.Interface focus · 2020Review
- Article
Corrections and comments
- Comment on
- Comment on
Authors and funding
5 authors.
Funding
Abstract
We recently reported that molecular dynamics simulations for hemoglobin require a surprisingly large box size to stabilize the T(0) state relative to R(0), as observed in experiments (El Hage et al., 2018). Gapsys and de Groot have commented on this work but do not provide convincing evidence that the conclusions of El Hage et al., 2018 are incorrect. Here we respond to these concerns, argue that our original conclusions remain valid, and raise our own concerns about some of the results reported in the comment by Gapsys and de Groot that require clarification.
Indexed as
Identifiers
What OpenQuestion holds
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.