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  1. Article ; Online: Structure of POPC Lipid Bilayers in OPLS3e Force Field.

    Kurki, Milla / Poso, Antti / Bartos, Piia / Miettinen, Markus S

    Journal of chemical information and modeling

    2022  

    Abstract: It is crucial for molecular dynamics simulations of biomembranes that the force field parameters give a realistic model of the membrane behavior. In this study, we examined the OPLS3e force field for the carbon-hydrogen order ... ...

    Abstract It is crucial for molecular dynamics simulations of biomembranes that the force field parameters give a realistic model of the membrane behavior. In this study, we examined the OPLS3e force field for the carbon-hydrogen order parameters
    Language English
    Publishing date 2022-08-31
    Publishing country United States
    Document type Journal Article
    ZDB-ID 190019-5
    ISSN 1549-960X ; 0095-2338
    ISSN (online) 1549-960X
    ISSN 0095-2338
    DOI 10.1021/acs.jcim.2c00395
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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  2. Article ; Online: Overlay databank unlocks data-driven analyses of biomolecules for all.

    Kiirikki, Anne M / Antila, Hanne S / Bort, Lara S / Buslaev, Pavel / Favela-Rosales, Fernando / Ferreira, Tiago Mendes / Fuchs, Patrick F J / Garcia-Fandino, Rebeca / Gushchin, Ivan / Kav, Batuhan / Kučerka, Norbert / Kula, Patrik / Kurki, Milla / Kuzmin, Alexander / Lalitha, Anusha / Lolicato, Fabio / Madsen, Jesper J / Miettinen, Markus S / Mingham, Cedric /
    Monticelli, Luca / Nencini, Ricky / Nesterenko, Alexey M / Piggot, Thomas J / Piñeiro, Ángel / Reuter, Nathalie / Samantray, Suman / Suárez-Lestón, Fabián / Talandashti, Reza / Ollila, O H Samuli

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 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 ... ...

    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.
    MeSH term(s) Artificial Intelligence ; Cell Membrane ; Membrane Lipids ; Molecular Dynamics Simulation ; Machine Learning
    Chemical Substances Membrane Lipids
    Language English
    Publishing date 2024-02-07
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-024-45189-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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