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  • Supporting data: Domain-agnostic predictions of nanoscale interactions in proteins and nanoparticles

    work
    Creator:
    Saldinger, Jacob, Raymond, Matt , Elvati, Paolo, and Violi, Angela
    Description:
    The accurate and rapid prediction of generic nanoscale interactions is a challenging problem with broad applications. Much of biology functions at the nanoscale, and our ability to manipulate materials and purposefully engage biological machinery requires knowledge of nano-bio interfaces. While several protein-protein interaction models are available, they leverage protein-specific information, limiting their abstraction to other structures. Here, we present NeCLAS, a general, and rapid machine learning pipeline that predicts the location of nanoscale interactions, providing human-intelligible predictions. Two key aspects distinguish NeCLAS: coarse-grained representations, and the use of environmental features to encode the chemical neighborhood. We showcase NeCLAS with challenges for protein-protein, protein-nanoparticle and nanoparticle-nanoparticle systems, demonstrating that NeCLAS replicates computationally- and experimentally-observed interactions. NeCLAS outperforms current nanoscale prediction models, and it shows cross-domain validity, qualifying as a tool for basic research, rapid prototyping, and design of nanostructures., Software: - To reproduce all-atom molecular dynamics (MD) NAMD is required (version 2.14 or later is suggested). NAMD software and documentation can be found at  https://www.ks.uiuc.edu/Research/namd/, - To reproduce coarse-grained MD simulations, LAMMPS (version 29 Sep 2021 - Update 2 or later is suggested). LAMMPS software and documentation can be found at  https://www.lammps.org, - To rebuild free energy profiles, the PLUMED plugin (version 2.6) was used. PLUMED software and documentation can be found at  https://www.plumed.org/ , and - To generate force matching potentials, the was used the OpenMSCG software was used. OpenMSCG software and documentation can be found at  https://software.rcc.uchicago.edu/mscg/
    Keyword:
    Neural Networks, Proteins, Dimensionality Reduction, Nanoparticles, and Coarse-Graining
    Citation to related publication:
     https://www.biorxiv.org/content/10.1101/2022.08.09.503361v2
    Discipline:
    Science