MD simulation data for Activation and substrate specificity of the human P4-ATPase ATP8B1

This repository contains MD simulation data and analysis scripts to recreate the analysis of the simulations in the corresponding publication: "Activation and substrate specificity of the human P4-ATPase ATP8B1" Thibaud Dieudonné (a), Felix Kümmerer ), Michelle Juknaviciute Laursen (a), Charlott Stock(a), Rasmus Kock Flygaard (a), Syma Khalid (c), Guillaume Lenoir (d), Joseph A. Lyonn s (e), Kresten Lindorff-Larsen (b) and Poul Nissen (a). (a) DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark (b) Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Denmark (c) Department of Biochemistry, University of Oxford, Oxford, United Kingdom (d) Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France (e) Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark Content: - All required files and parameters to setup and rerun the equilibration and production simulations using GROMACS - The MD trajectories of all particles in .xtc format saved every 1 ns: 5x 600 ns per system (PIP bound and PIP3 bound) - Processed trajectories and structure files used in the analysis - Some intermediate data for the analysis (instructions on how to obtain these is described in the notebook + paper) - Jupyter Notebook with all the analysis to recreate the figures based on MD data in the main text and supplementary information of the paper