MD simulations data for Hirschi et al. (2024)

This repository contains the initial coordinates and final output coordinate files for Molecular Dynamics (MD) simulations. The data is organized and named according to the following convention:

PDB ID of Seeding Structure: Identifier of the protein structure used to initiate the simulation.

Type of Ligand: Indicates the presence and type of ligand bound to the protein.

schiff: Retinal forming a Schiff base

dka: Decanoate

apo: No ligand

Replica Number: Number assigned to each independent simulation run (1, 2, or 3).

Simulation Stage: Indicates whether the file corresponds to the initial structure (0) or the final frame of the simulation (final).

Example File Names:

7B03_apo_3_final.pdb: Final frame of the third replica simulation of the apo state of the protein with PDB ID 7B03.

7B03_schiff_1_0.pdb: Initial structure of the first replica simulation with a Schiff base ligand for the protein with PDB ID 7B03.

Simulation Details:

Replica 1: A long simulation with a duration of 950 nanoseconds (ns).

Replicas 2 and 3: Two shorter simulations, each lasting 400 ns.