Overlay databank unlocks data-driven analyses of biomolecules for all

Anne M. Kiirikki, Hanne S. Antila, Lara S. Bort, Pavel Buslaev, Fernando Favela-Rosales, Tiago Mendes Ferreira, Patrick F. J. Fuchs, Rebeca Garcia-Fandino, Ivan Gushchin, Batuhan Kav, Norbert Kučerka, Patrik Kula, Milla Kurki, Alexander Kuzmin, Anusha Lalitha, Fabio Lolicato, Jesper J. Madsen, Markus S. Miettinen, Cedric Mingham, Luca Monticelli, Ricky Nencini, Alexey M. Nesterenko, Thomas J. Piggot, Ángel Piñeiro, Nathalie Reuter, Suman Samantray, Fabián Suárez-Lestón, Reza Talandashti and O. H. Samuli Ollila ()
Additional contact information
Anne M. Kiirikki: University of Helsinki, Institute of Biotechnology
Hanne S. Antila: Max Planck Institute of Colloids and Interfaces
Lara S. Bort: Max Planck Institute of Colloids and Interfaces
Pavel Buslaev: University of Jyväskylä
Fernando Favela-Rosales: Tecnológico Nacional de México - ITS Zacatecas Occidente
Tiago Mendes Ferreira: Martin Luther University Halle-Wittenberg
Patrick F. J. Fuchs: PSL University, CNRS, Laboratoire des Biomolécules (LBM)
Rebeca Garcia-Fandino: Universidade de Santiago de Compostela
Batuhan Kav: Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich
Norbert Kučerka: Comenius University Bratislava
Patrik Kula: Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
Milla Kurki: University of Eastern Finland
Anusha Lalitha: Université Montpellier
Fabio Lolicato: Heidelberg University Biochemistry Center
Jesper J. Madsen: University of South Florida
Markus S. Miettinen: Max Planck Institute of Colloids and Interfaces
Cedric Mingham: University of Applied Sciences
Luca Monticelli: University of Lyon, CNRS, Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086)
Ricky Nencini: University of Helsinki, Institute of Biotechnology
Alexey M. Nesterenko: University of Bergen
Thomas J. Piggot: University of Southampton
Ángel Piñeiro: University of Santiago de Compostela
Nathalie Reuter: University of Bergen
Suman Samantray: Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich
Fabián Suárez-Lestón: Universidade de Santiago de Compostela
Reza Talandashti: University of Bergen
O. H. Samuli Ollila: University of Helsinki, Institute of Biotechnology

Nature Communications, 2024, vol. 15, issue 1, 1-15

Abstract: 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.

Date: 2024
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DOI: 10.1038/s41467-024-45189-z

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