High-resolution mining of the SARS-CoV-2 main protease conformational space: supercomputer-driven unsupervised adaptive sampling
Théo Jaffrelot Inizan, Frédéric Célerse, Olivier Adjoua, Dina El Ahdab, Luc-Henri Jolly, Chengwen Liu, Pengyu Ren, Matthieu Montès, Nathalie Lagarde, Louis Lagardère, Pierre Monmarché, Jean‐Philip Piquemal
Abstract
We provide an unsupervised adaptive sampling strategy capable of producing μs-timescale molecular dynamics (MD) simulations of large biosystems using many-body polarizable force fields (PFFs).
Topics & Concepts
Molecular dynamicsOxyanion holeCluster analysisAdaptive samplingComputer scienceSampling (signal processing)Biological systemPipeline (software)ChemistryPhysicsComputational chemistryActive siteMonte Carlo methodArtificial intelligenceMathematicsBiologyEnzymeComputer visionStatisticsProgramming languageBiochemistryFilter (signal processing)Protein Structure and DynamicsMachine Learning in Materials ScienceRNA and protein synthesis mechanisms