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

Overview

This archive (3/3) contains the results (kith, nram and streptavidin) 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)