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Showing 1–6 of 6 results
Advanced filters: Author: Stefano Raniolo Clear advanced filters

  • Computer-aided design of protein-ligand binding is important for the development of novel drugs. Here authors present an approach to use the recently re-parametrized coarse-grained Martini model to perform unbiased millisecond sampling of protein-ligand binding interactions of small drug-like molecules.

    • Paulo C. T. Souza
    • Sebastian Thallmair
    • Siewert J. Marrink
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-11

  • Here, authors report chemokine receptors structures obtained using coarse-grained metadynamics. CCR5 and CXCR4 homo- and heterodimers differ in the conformations of ligand binding sites and of the G protein interaction interface, suggesting structural basis for the rational design of biased ligands.

    • Daniele Di Marino
    • Paolo Conflitti
    • Vittorio Limongelli
    ResearchOpen Access
    Nature Communications
    Volume: 14, P: 1-16

  • The binding interaction between the Shelterin complex protein TPP1 and the human telomerase enzyme can trigger telomerase maintenance, however, the conformational change of TPP1 functional for binding remains underexplored. Here, the authors characterize the structural properties of a group of amino acids named the TEL-patch within TPP1’s oligosaccharide/oligonucleotide-domain by molecular dynamics simulation, time-series analyses, and graph-based networks, revealing their conformational plasticity and allosteric communication networks.

    • Simone Aureli
    • Vince Bart Cardenas
    • Vittorio Limongelli
    ResearchOpen Access
    Communications Chemistry
    Volume: 6, P: 1-10

  • Machine learning algorithms are widely employed for molecular simulations, but there are likely many yet unexplored routes for the prediction of structural and energetic properties of biologically relevant systems. Here, the authors develop a hypergraph representation and message passing method for transferring knowledge obtained from simple molecular systems onto more complex ones, demonstrated by transfer learning from tri-alanine to the deca-alanine system.

    • Sajjad Heydari
    • Stefano Raniolo
    • Vittorio Limongelli
    ResearchOpen Access
    Communications Chemistry
    Volume: 6, P: 1-13

  • Here the authors describe a GUI-based protocol called FMAP for using funnel metadynamics to calculate the absolute binding free energy of a ligand to its molecular target and predict the ligand binding mode and mechanism.

    • Stefano Raniolo
    • Vittorio Limongelli
    Protocols
    Nature Protocols
    Volume: 15, P: 2837-2866

  • The PLUMED consortium unifies developers and contributors to PLUMED, an open-source library for enhanced-sampling, free-energy calculations and the analysis of molecular dynamics simulations. Here, we outline our efforts to promote transparency and reproducibility by disseminating protocols for enhanced-sampling molecular simulations.

    • Massimiliano Bonomi
    • Giovanni Bussi
    • Andrew White
    Comments & Opinion
    Nature Methods
    Volume: 16, P: 670-673