ArticleJournal of physics. Conference series2018
High-Performance Data Analysis on the Big Trajectory Data of Cellular Scale All-atom Molecular Dynamics Simulations.
Article in Journal of physics. Conference series, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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Who cites it
7 citing papers in PubMed.
- mdBIRCH for Fast, Scalable, Online Clustering of Molecular Dynamics Trajectories.bioRxiv : the preprint server for biology · 2025Article
- Systematic analysis, aggregation and visualisation of interaction fingerprints for molecular dynamics simulation data.Journal of cheminformatics · 2024Article
- SINAPs: A Software Tool for Analysis and Visualization of Interaction Networks of Molecular Dynamics Simulations.Journal of chemical information and modeling · 2022Article
- Reduced efficacy of a Src kinase inhibitor in crowded protein solution.Nature communications · 2021Article
- Whole-Cell Models and Simulations in Molecular Detail.Annual review of cell and developmental biology · 2019Review
- An implicit lipid model for efficient reaction-diffusion simulations of protein binding to surfaces of arbitrary topology.The Journal of chemical physics · 2019Article
- A Machine Learning Approach for the Discovery of Ligand-Specific Functional Mechanisms of GPCRs.Molecules (Basel, Switzerland) · 2019Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The inside of a cell is highly crowded with a large number of macromolecules together with solvents and metabolites. To know the molecular-level behaviour of biomolecules in such dense crowding environment, we constructed full atomistic model of the cytoplasm of bacteria, and performed massive all-atom molecular dynamics (MD) simulations. On the other hand, to analyse such big MD data, we need significant computational power and efficient calculation methodology. Here, we introduce what and how we analyse the biomolecule properties from the big trajectory data produced by cellular scale all-atom MD simulations.
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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.