CITATION.cff

cff-version: 1.2.1
title: FAIRMD BilayerData
message: >-
  If you use this dataset, please cite it using the metadata
  from this file.
type: dataset
authors:
  - name: larabort
    family-names: Dautzenberg
    given-names: Lara
  - name: comcon1
    family-names: Nesterenko
    given-names: Alexey
  - name: ohsOllila
    family-names: Ollila
    given-names: O. H. Samuli
  - name: korbinib
    family-names: Bösl
    given-names: Korbinian
    orcid: https://orcid.org/0000-0003-0498-4273  
  - name: MagnusSletten
    family-names: Sletten
    given-names: Magnus-Elias
  - name: batukav
    family-names: Kav
    given-names: Batuhan
  - name: markussmiettinen
    family-names: Miettinen
    given-names: Markus
  - names: tfmFerreira 
    family-names: Ferreira
    given-names: Tiago Mendes
  - name: akiirik
    family-names: Kiirikki
    given-names: Anne  
  - name: ferdi385
    family-names: Hörstel
    given-names: Ferdinand
  - name: PEFrankel
    family-names: Frankel
    given-names: Patrick
  - name: Avneesh.Singh 
    family-names: Singh
    given-names: Avneesh
  - name: frgr2254
    family-names: Grote
    given-names: Frederik
  - name: thraindk
    family-names: Mingham
    given-names: Cedric
  - name: fsuarezleston
    family-names: Suárez-Lestón
    given-names: Fabián   
  - name: mdondrup
    family-names: Dondrup
    given-names: Michael  
  - name: jagdep-singh
    family-names: Singh
    given-names: Jagdeep  
  - name: ffavelar 
    family-names: Favela-Rosales
    given-names: Fernando
  - name: MelbourneFL
    family-names: Vogel
    given-names: Alexander
  - name: awurl
    family-names: Wurl
    given-names: Anika
  - name: JHoeflich1
    family-names: Hoeflich
    given-names: Julianne
  - name: hseara
    family-names: Monne
    given-names: Hector Martinez-Seara
  - name: pbuslaev
    family-names: Buslaev
    given-names: Pavel
  - name: suviheinonen
    family-names: Heinonen
    given-names: Suvi
identifiers:
  - type: url
    value: >-
      https://github.com/NMRLipids/BilayerData/releases/tag/v1.3.3
    description: The URL of version 1.3.3 of the dataset
repository-code: 'https://github.com/NMRLipids/BilayerData'
repository: 'https://databank.nmrlipids.fi/'
abstract: >-
  FAIRMD BilayerData is an on-github database of quality-evaluated lipid bilayer structures operated by the FAIRMD Lipids Project. The database contains information
  about:
  experiments, namely form factor data from Small-Angle X-ray Scattering (SAXS) experiments and order parameter data from 1H-13C dipolar splitting or from 2H quadrupolar splitting NMR experiments
  MD simulations, run by different engines using various force fields the molecules included in the experimental and simulation compositions, along with atom namings in different force fields and detailed metadata for each

  The database doesn't store raw simulation or experiment data; it uses an overlay databank approach, i.e., stores only links to public archives like Zenodo, where complete MD trajectories must be stored. The database structure is described in detail in the FAIRMD Lipids documentation.
  All the simulations from this database are mirrored at the NMRlipids webUI.

license: CC-BY-4.0
commit: 3e26622538bfb3f0da7b51f5e9641a870441aa35
version: 1.3.3
date-released: '2020-01-08'
preferred-citation:
  type: article
  authors:
    - family-names: Kiirikki
      given-names: Anne M.
    - family-names: Antila
      given-names: Hanne S.
    - family-names: Bort
      given-names: Lara S.
    - family-names: Buslaev
      given-names: Pavel
    - family-names: Favela-Rosales
      given-names: Fernando
    - family-names: Ferreira
      given-names: Tiago Mendes
    - family-names: Fuchs
      given-names: Patrick F. J.
    - family-names: Garcia-Fandino
      given-names: Rebeca
    - family-names: Gushchin
      given-names: Ivan
    - family-names: Kav
      given-names: Batuhan
    - family-names: Kučerka
      given-names: Norbert
    - family-names: Kula
      given-names: Patrik
    - family-names: Kurki
      given-names: Milla
    - family-names: Kuzmin
      given-names: Alexander
    - family-names: Lalitha
      given-names: Anusha
    - family-names: Lolicato
      given-names: Fabio
    - family-names: Madsen
      given-names: Jesper J.
    - family-names: Miettinen
      given-names: Markus S.
    - family-names: Mingham
      given-names: Cedric
    - family-names: Monticelli
      given-names: Luca
    - family-names: Nencini
      given-names: Ricky
    - family-names: Nesterenko
      given-names: Alexey M.
    - family-names: Piggot
      given-names: Thomas J.
    - family-names: Piñeiro
      given-names: Ángel
    - family-names: Reuter
      given-names: Nathalie
    - family-names: Samantray
      given-names: Suman
    - family-names: Suárez-Lestón
      given-names: Fabián
    - family-names: Talandashti
      given-names: Reza
    - family-names: Ollila
      given-names: O. H. Samuli
  title: Overlay Databank Unlocks Data-Driven Analyses of Biomolecules for All
  journal: Nature Communications
  volume: 15
  issue: 1
  pages: 1136
  year: 2024
  month: 2
  issn: 2041-1723
  doi: 10.1038/s41467-024-45189-z
  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.