ArticleNature communications2024
Overlay databank unlocks data-driven analyses of biomolecules for all.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers, 1 of them a synthesis that pooled it.
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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.
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Who cites it
18 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-Analysis of Permeability Literature Data Shows Possibilities and Limitations of Popular Methods.Molecular pharmaceutics · 2025Pooled it
- Determination of water permeability in stress-free lipid membranes through time-resolved small-angle neutron scattering.Journal of applied crystallography · 2026Article
- SuAVE-Scatter: A Module for Integrating Simulations and SAXS/SANS Analyses.Journal of chemical information and modeling · 2026Article
- Molecular dynamics simulation in traditional Chinese medicine research: from molecular mechanisms to multiscale validation.Frontiers in chemistry · 2026Review
- Optimizing a coarse-grained model for large-scale membrane protein simulation.Biophysical reports · 2025Article
- Quality Evaluation Based Simulation Selection (QEBSS) for analysis of conformational ensembles and dynamics of multidomain proteins.Communications chemistry · 2025Article
- Article
- Free Energy of Membrane Pore Formation and Stability from Molecular Dynamics Simulations.Journal of chemical information and modeling · 2025Article
- Solid-State NMR Validation of OPLS4: Structure of PC-Lipid Bilayers and Its Modulation by Dehydration.The journal of physical chemistry. B · 2024Article
- Simulating Bacterial Membrane Models at the Atomistic Level: A Force Field Comparison.Journal of chemical theory and computation · 2024Article
- Effective Inclusion of Electronic Polarization Improves the Description of Electrostatic Interactions: The prosECCo75 Biomolecular Force Field.Journal of chemical theory and computation · 2024Article
- Signal peptidase SpsB coordinates staphylococcal cell cycle, surface protein septal trafficking and LTA synthesis.bioRxiv : the preprint server for biology · 2024Article
- Pathways to a Shiny Future: Building the Foundation for Computational Physical Chemistry and Biophysics in 2050.ACS physical chemistry Au · 2024Review
- Interaction of MRI Contrast Agent [Gd(DOTA)]Inorganic chemistry · 2024Article
- Evaluating Polarizable Biomembrane Simulations against Experiments.Journal of chemical theory and computation · 2024Article
- Efficient calculation of orientation-dependent lipid dynamics from membrane simulations.bioRxiv : the preprint server for biology · 2024Article
- Probing the dynamic landscape of peptides in molecular assemblies by synergized NMR experiments and MD simulations.Communications chemistry · 2024Article
- Membrane binding and lipid-protein interaction of the C2 domain from coagulation factor V.Current research in structural biology · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
29 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Tools based on artificial intelligence (AI) are currently revolutionising many fields, yet their applications are often limited by the lack of suitable training data in programmatically accessible format. Here we propose an effective solution to make data scattered in various locations and formats accessible for data-driven and machine learning applications using the overlay databank format. To demonstrate the practical relevance of such approach, we present the NMRlipids Databank-a community-driven, open-for-all database featuring programmatic access to quality-evaluated atom-resolution molecular dynamics simulations of cellular membranes. Cellular membrane lipid composition is implicated in diseases and controls major biological functions, but membranes are difficult to study experimentally due to their intrinsic disorder and complex phase behaviour. While MD simulations have been useful in understanding membrane systems, they require significant computational resources and often suffer from inaccuracies in model parameters. Here, we demonstrate how programmable interface for flexible implementation of data-driven and machine learning applications, and rapid access to simulation data through a graphical user interface, unlock possibilities beyond current MD simulation and experimental studies to understand cellular membranes. The proposed overlay databank concept can be further applied to other biomolecules, as well as in other fields where similar barriers hinder the AI revolution.
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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.