Replication Data for: "Atomistic description of the OCTN1 recognition mechanism via in silico methods"

Replication Data for "Atomistic description of the OCTN1 recognition mechanism via in silico methods, PLOS ONE, 2024, 19(6): e0304512".

The dataset includes two distinct types of PDB files, identified by their naming convention.
1. Docking poses
Files:
22a4_*_pose.pdb
Description:
These files contain the docking poses of individual ligands bound to OCTN1. Each PDB file corresponds to a different compound (indicated by * in the file name) and represents the selected binding pose obtained from molecular docking calculations. The structures include OCTN1 and the docked ligand in the predicted binding configuration.
Docking poses are useful to reproduce MD simulations.
2. MD equilibration cluster medoids
Files:
r1_22a4_*.pdb
r2_22a4_*.pdb
Description:
These files contain representative structures (medoids) of conformational clusters extracted from independent equilibration molecular dynamics replicas of OCTN1–ligand complexes.
The prefix r1 and r2 identifies different MD replicas, while * denotes the ligand name. For each ligand, the medoid corresponds to the most representative structure of the dominant cluster sampled during the equilibration phase, and captures the stabilized binding mode of the compound within OCTN1.
MD clusters are useful to asses the rearrangements of the complexes.