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)