Repository of atomistic simulations of GPR68
This public repository contains restart files and simulations used for the publication ''Protons Taken Hostage: Dynamic H-Bond Network of pH-sensing GPR68". Authors: Bhav Kapur, Filippo Baldessari, Michalis Lazaratos, Herbert Nar, Gisela Schnapp, Alejandro Giorgetti, Ana-Nicoleta Bondar. Contents The repository includes: 1. Simulation data: Atomistic NAMD simulation files (.dcd), protein structure files (.psf) and protein data bank files (.pdb) and restart files for GPR68 structural model (1µs), GPR68 Structural Model in 10% Cholesterol (600ns) and 9 different protonation simulations (600ns each) using the best GPR68 model. Note: The trajectory files (.dcd) in this repository were written every 1ns and only the last 100ns from all the simulations have been uploaded. 2. The nine structural models described in the manuscript. 3. Sequence Alignment files for Figure 1B of the manuscript, proton-sensing GPCRs (GPR68, GPR4, GPR65, GPR132, GPR31, and GPR151), and whole class A GPCR family (312 sequences). Contact For questions regarding the repository, or to request additional coordinate sets from the simulation trajectories reported in the paper, please contact the repository owner at email@example.com or firstname.lastname@example.org.
H2020 Marie Skłodowska-Curie Actions