Data set for validation of a Python script for computation of Protein-Ligand Interaction Fingerprints

Data set for  for validation of the Protein-Ligand Interaction Fingerprints, which includes examples of protein structures  (original PDB and equilibrated) and molecular dynamics trajectories (equilibration and ligand dissociation generated using Random Acceleration MD simulations, RAMD)

2YKI - protein-ligand complex , PDB ID 2YKI
   - 2yki_MOE.pdb complex with hydrogen added and energy minimized using MOE software (https://www.chemcomp.com/)
   -  ligand_2yki_MOE.mol2 and ligand_2yki_MOE.pdb - ligand structure with hydrogens prepered by MOE software (https://www.chemcomp.com/)

6EI5 - MD trajectory of the protein-ligand complex generated from PDB ID 6EI5
   - ref-min.pdb  minimized structure
   - ref.prmtop topology file
   - moe.mol2 - ligand structure in mol2 format
   - amber2namd2.dcd generated MD trajectory 

The rest of the files contains data obtained from simulation of the complex of GPCR muscarinic receptor M2 (PDB ID:4MQT; immersed in a mixed membrane: 50% CHL, 30% POPC, 20% POPE)  with a small molecule agonist iperoxo. 
   - IXO.pdb and moe.mol2 - PDBand MOL2 structure of iperoxo
   - AMBER_eq.tar.gz - structure of the equilibrated complex generated using AMBER software
   - NAMD_eq.tar.gz - two equilibration trajectories in dcd format generated using NAMD software 
   - RAMD_eq.tar.gz - dissociation tarjectoris of iprtoxo from the M2 protein generated from the last snapshot of two NAMD equilibration trajectories (for each case 2 RAMD dissociaiton trajectories are available) 


SAD_3-RAMD-03-2020.pkl - a pkl dataset with IFPs generated from RAMD dissociation trajectory of the complex PDB ID: 5LQ9 (trajectories from the paper Front. Mol. Biosci., 2019 DOI:10.3389/fmolb.2019.00036