Data supporting "Machine Learning-based Modeling of Olfactory Receptors: Human OR51E2 as a Case Study"

Simulation data and input files in support of the Manuscript:"Machine Learning-based Modeling of Olfactory Receptors: Human OR51E2 as a Case Study".

The archive is organized in 6 different folders:

1. 7x7_rmsd, which contains a tcl script (to be run in VMD) to compute the 7x7 RMSD matrix (see Wang et al. J Struct. Bio, (2017)).
2. a100_plumed, which contains PLUMED input files to compute A¹⁰⁰ index on OR51E2 trajectories.
3. initial_structures, which contains the 6 different conformation for hOR51E2 obtained by the different predictors in the pdb format.
4. mdp_files, which contains the GROMACS mdp files to perform all the protocol described in the paper.
5. topologies, which contains the 6 different topologies (in .top format) and the initial conformation (in .gro format) for the hOR51E2 embedded in the membrane and solvated.
6. trajectories, which contains the 18 (6 systems, 3 replicas per system) different trajectories with the sodium in place close to D69^2.50 without solvent and ions (in .xtc format with a frame every 100 ps) and a reference conformation (in .gro format). Here we have also added the trajectory for the SwissModel-derived simulation without sodium ion in place, where we observed the ion binding. This last trajectory contains also solvent and ions, but with a lower printing frequency (1 ns).