All-atom molecular dynamics simulation and rate calculation for norepinephrine binding beta adrenergic receptor

This dataset is for the manuscript \"A multiscale predictive digital twin for neurocardiac modulation\". We utilized all-atom molecular dynamics (MD) simulations to predict the affinities as well as association and dissociation rates of norepinephrine (NE) with the beta-2 adrenergic receptor (β2AR). Calculations were done for both cationic (+) and neutral (0) forms of NE. An active-state β2AR model based on its crystal structure PDB ID: 4LDO was used with the flexible intracellular loop 3 (ICL3) truncated to 3 residues. ROSETTALIGAND was used for docking NE(+) and NE(0) to the receptor's orthosteric ligand binding site with one of the top scoring models used for MD simulations. MD simulation systems of the NE(+) or NE(0) bound β2AR receptor embedded in a palmitoyloleoylphosphatidylcholine (POPC) bilayer solvated by aqueous 0.15 M NaCl was generated using CHARMM-GUI membrane builder. MD simulations were run with NAMD in the NPT ensemble at 310 K and 1 atm pressure using CHARMM36m force fie..., ,