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Showing 1–4 of 4 results
Advanced filters: Author: Vytautas Gapsys Clear advanced filters

  • Relative binding free energy calculations are widely used to guide drug discovery by accurately computing binding affinity, however, these simulations remain complicated to set up, computationally expensive to run, and technically challenging to scale up. Here, the authors develop an end-to-end relative free energy workflow based on a non-equilibrium switching approach that calculates the binding free energies starting from SMILES strings.

    • J. Harry Moore
    • Christian Margreitter
    • Vytautas Gapsys
    ResearchOpen Access
    Communications Chemistry
    Volume: 6, P: 1-12

  • Molecular dynamics-based approaches to calculate absolute protein–ligand binding free energy often rely on equilibrium free energy perturbation (FEP) protocols. Here, the authors study ligands binding to bromodomains and T4 lysozyme and find that both equilibrium and non-equilibrium approaches converge to the same results with the non-equilibrium method converging faster than FEP.

    • Vytautas Gapsys
    • Ahmet Yildirim
    • Bert L. de Groot
    ResearchOpen Access
    Communications Chemistry
    Volume: 4, P: 1-13

  • The authors provide a litmus test for the recognition mechanism of transiently binding proteins based on nuclear magnetic resonance and find a conformational selection binding mechanism through concentration-dependent kinetics of ubiquitin and SH3.

    • Kalyan S. Chakrabarti
    • Simon Olsson
    • Christian Griesinger
    ResearchOpen Access
    Nature Communications
    Volume: 13, P: 1-11