WaterKit: thermodynamic profiling of protein hydration sites (2/3)

Overview

This archive (2/3) contains the results (fa10 and pgh2) for the following study:

WaterKit: thermodynamic profiling of protein hydration sites (https://doi.org/10.26434/chemrxiv-2022-grlsr)

Each zip archive contains the following files:

charmm-gui: output from CHARMM-gui

xx_amber: GIST output from MD simulations

figures: convergence, predictions per waterkit model plots, etc...

pdbbind_ligands: contains all the ligands used to define the ligand binding site

waterkit: contains all the results from the WaterKit calculations

All the WaterKit parameters tested:

ad : acceptor/donor anchor points

all : used all hydrogen atoms as anchor points

vina : used O_DA vina probe for the spherical model (otherwise TIP3P model)

300 : temperature

3 : number of hydration layers placed during the calculations

min_100_2.5 : 100 steps of minimization with 2.5 kcal/mol/A**2 constraints

Each directory contains:

output from the GIST analysis (gist-*.dx)

cluster.pdb: All the hydration sites identified

protein.nc : WaterKit "trajectory"

protein_system.prmtop : Amber top file

pymol_*.pse : PyMol session with all the results (WK, MD)

results_*.png : Comparison plots between WaterKit predictions and MD simulations per hydration sites

analysis_xxx.ipynb: Jupyter notebook containing all the analysis (needs utils.py file)

protein_prepared.pdbqt: structure used for the WK calculations

results_md.csv : contains all the raw results from the MD simulations

results_wk.csv : contains all the raw results from the WK calculations

results_md_md_comp_energy_*.csv : comparison results between MD simulations (energy)

results_md_md_comp_placement_*.csv : comparison results between MD simulations (placement)

results_md_wk_comp_energy_*.csv : comparison results between MD simulations and WK (energy)

results_md_wk_comp_placement_*.csv : comparison results between MD simulations and WK (placement)

results_wk_wk_comp_energy_*.csv : comparison results between WK calculations (energy)

results_wk_wk_comp_placement_*.csv : comparison results between WK calculations (placement)