ArticleeLife2024
MDverse, shedding light on the dark matter of molecular dynamics simulations.
Article in eLife, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 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
20 citing papers in PubMed.
- Modeling conformational transitions in DNA, RNA, and protein-nucleic acid complexes.Nucleic acids research · 2026Article
- Advances and challenges in multiscale biomolecular simulations: artificial intelligence-driven paradigm shift.Quantitative biology (Beijing, China) · 2026Article
- Human class B1 GPCR modulation by plasma membrane lipids.Communications biology · 2026Article
- DynaRepo: the repository of macromolecular conformational dynamics.Nucleic acids research · 2026Article
- Molecular dynamics simulation in traditional Chinese medicine research: from molecular mechanisms to multiscale validation.Frontiers in chemistry · 2026Review
- Atomistic Polymer Modeling: Recent Advances and Challenges in Building and Parametrization Workflows.Macromolecules · 2025Review
- Gromacs MetaDump: a tool for extracting GROMACS simulation metadata.Journal of cheminformatics · 2025Article
- PEGASUS: Prediction of MD-derived protein flexibility from sequence.Protein science : a publication of the Protein Society · 2025Article
- mdciao: Accessible Analysis and Visualization of Molecular Dynamics Simulation Data.PLoS computational biology · 2025Article
- A FAIR-Compliant Management Solution for Molecular Simulation Trajectories.Journal of chemical information and modeling · 2025Article
- The Influence of Phosphoinositide Lipids in the Molecular Biology of Membrane Proteins: Recent Insights from Simulations.Journal of molecular biology · 2025Review
- Permeability Benchmarking: Guidelines for ComparingJournal of chemical information and modeling · 2025Review
- Pathways to a Shiny Future: Building the Foundation for Computational Physical Chemistry and Biophysics in 2050.ACS physical chemistry Au · 2024Review
- Probing the dynamic landscape of peptides in molecular assemblies by synergized NMR experiments and MD simulations.Communications chemistry · 2024Article
- Overlay databank unlocks data-driven analyses of biomolecules for all.Nature communications · 2024Article
- Multi-Journal of chemical theory and computation · 2024Article
- One bead per residue can describe all-atom protein structures.Structure (London, England : 1993) · 2024Article
- From complex data to clear insights: visualizing molecular dynamics trajectories.Frontiers in bioinformatics · 2024Review
- VIAMD: a Software for Visual Interactive Analysis of Molecular Dynamics.Journal of chemical information and modeling · 2023Article
- Machine Learning-Guided Protein Engineering.ACS catalysis · 2023Review
Corrections and comments
- Update of
Authors and funding
12 authors.
Funding
Abstract
The rise of open science and the absence of a global dedicated data repository for molecular dynamics (MD) simulations has led to the accumulation of MD files in generalist data repositories, constituting the
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.