Overlay databank unlocks data-driven analyses of biomolecules for all
Nature Communications, vol. 15, pp. 1136
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.
Authors 29
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Affiliation as printed
University of Helsinki, Institute of Biotechnology, Helsinki, Finland
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Max Planck Institute of Colloids and Interfaces · University of Bergen
Affiliation as printed
Department of Biomedicine, University of Bergen, 5020, Bergen, Norway
Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14424, Potsdam, Germany
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University of Potsdam · Max Planck Institute of Colloids and Interfaces
Affiliation as printed
Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14424, Potsdam, Germany
University of Potsdam, Institute of Physics and Astronomy, 14476, Potsdam-Golm, Germany
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Affiliation as printed
Nanoscience Center and Department of Chemistry, University of Jyväskylä, 40014, Jyväskylä, Finland
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Tecnológico Nacional de México
Affiliation as printed
Departamento de Ciencias Básicas, Tecnológico Nacional de México - ITS Zacatecas Occidente, Sombrerete, 99102, Zacatecas, Mexico
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Martin Luther University Halle-Wittenberg
Affiliation as printed
NMR group - Institute for Physics, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
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Centre National de la Recherche Scientifique · Université Paris Cité · Université Paris Sciences et Lettres · École Normale Supérieure - PSL · Sorbonne Université · Laboratoire des Biomolécules
Affiliation as printed
Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules (LBM), F-75005, Paris, France
Université Paris Cité, F-75006, Paris, France
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Universidade de Santiago de Compostela · Centro Singular de Investigación en Química Biológica y Materiales Moleculares
Affiliation as printed
Center for Research in Biological Chemistry and Molecular Materials (CiQUS), Universidade de Santiago de Compostela, E-15782, Santiago de Compostela, Spain
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Affiliation as printed
Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52428, Jülich, Germany
ariadne.ai GmbH (Germany), Häusserstraße 3, 69115, Heidelberg, Germany
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Comenius University Bratislava
Affiliation as printed
Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University Bratislava, 832 32, Bratislava, Slovakia
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Czech Academy of Sciences · Czech Academy of Sciences, Institute of Organic Chemistry and Biochemistry
Affiliation as printed
Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16610, Prague, Czech Republic
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Affiliation as printed
School of Pharmacy, University of Eastern Finland, 70211, Kuopio, Finland
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Centre National de la Recherche Scientifique · Institut Charles Gerhardt Montpellier
Affiliation as printed
Institut Charles Gerhardt Montpellier (UMR CNRS 5253), Université Montpellier, Place Eugène Bataillon, 34095, Montpellier, Cedex 05, France
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University of Helsinki · Heidelberg University
Affiliation as printed
Department of Physics, University of Helsinki, FI-00014, Helsinki, Finland
Heidelberg University Biochemistry Center, 69120, Heidelberg, Germany
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Affiliation as printed
Center for Global Health and Infectious Diseases Research, Global and Planetary Health, College of Public Health, University of South Florida, 33612, Tampa, FL, USA
Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 33612, Tampa, FL, USA
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Max Planck Institute of Colloids and Interfaces · University of Bergen
Affiliation as printed
Department of Chemistry, University of Bergen, 5007, Bergen, Norway
Department of Informatics, Computational Biology Unit, University of Bergen, 5008, Bergen, Norway
Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14424, Potsdam, Germany
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Technische Hochschule Mannheim
Affiliation as printed
Hochschule Mannheim, University of Applied Sciences, 68163, Mannheim, Germany
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Centre National de la Recherche Scientifique · Inserm · Microbiologie moléculaire et biochimie structurale
Affiliation as printed
Institut National de la Santé et de la Recherche Médicale (INSERM), Lyon, France
University of Lyon, CNRS, Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), F-69007, Lyon, France
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Affiliation as printed
Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014, Helsinki, Finland
University of Helsinki, Institute of Biotechnology, Helsinki, Finland
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Affiliation as printed
Department of Chemistry, University of Bergen, 5007, Bergen, Norway
Department of Informatics, Computational Biology Unit, University of Bergen, 5008, Bergen, Norway
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Affiliation as printed
Chemistry, University of Southampton, Highfield, SO17 1BJ, Southampton, UK
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Universidade de Santiago de Compostela
Affiliation as printed
Department of Applied Physics, Faculty of Physics, University of Santiago de Compostela, E-15782, Santiago de Compostela, Spain
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Affiliation as printed
Department of Chemistry, University of Bergen, 5007, Bergen, Norway
Department of Informatics, Computational Biology Unit, University of Bergen, 5008, Bergen, Norway
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Forschungszentrum Jülich · RWTH Aachen University
Affiliation as printed
Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52428, Jülich, Germany
Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
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Universidade de Santiago de Compostela · Centro Singular de Investigación en Química Biológica y Materiales Moleculares
Affiliation as printed
Center for Research in Biological Chemistry and Molecular Materials (CiQUS), Universidade de Santiago de Compostela, E-15782, Santiago de Compostela, Spain
Department of Applied Physics, Faculty of Physics, University of Santiago de Compostela, E-15782, Santiago de Compostela, Spain
MD.USE Innovations S.L., Edificio Emprendia, 15782, Santiago de Compostela, Spain
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Affiliation as printed
Department of Chemistry, University of Bergen, 5007, Bergen, Norway
Department of Informatics, Computational Biology Unit, University of Bergen, 5008, Bergen, Norway
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O. H. Samuli Ollila corresponding
University of Helsinki · VTT Technical Research Centre of Finland
Affiliation as printed
University of Helsinki, Institute of Biotechnology, Helsinki, Finland. samuli.ollila@helsinki.fi
VTT Technical Research Centre of Finland, Espoo, Finland. samuli.ollila@helsinki.fi
VTT Technical Research Centre of Finland, Espoo, Finland
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