Water will find a way: transport through narrow tunnels in hydrolases (hEpx protein)

Water will find a way: transport through narrow tunnels in hydrolases (hEpx protein)

The input files and results used for the paper "Water will find a way: transport through narrow tunnels in hydrolases" are separated in the different files depending the stage they belong to.

01_Simulations.tar.gz: All the files used to get the data employing Molecular Dynamics simulations.

02_Caver.tar.gz: Caver config used together with the "Divide-and-conquer approach to study protein tunnels in long molecular dynamics simulations" method (https://doi.org/10.1016/j.mex.2022.101968), and after re-clustering as described in the methods section of the paper.

03_Aquaduct.tar.gz: Aquaduct results for all the MD trajectories.

04_TransportTools.tar.gz: TransportTools results for hEpx and E470G systems together, since we employed the comparative approach to analyze the results with TransportTools (https://doi.org/10.1093/bioinformatics/btab872).

05_WaterAnalysis.tar.gz: The results from the exact matching analysis were parsed to perform H-bond analysis. Here are the PDBs where the *minimum sphere event* is present. Also the txt files with the results from the H-bond analysis are here.

Files

01_build_database.py Python3 script to parse the results from the exact matching analysis from TransportTools into a dictionary of transport events. For more detailed information read the script documentation.

hEpx_E470G.dat Parsed database of transport events for hEpx_E470G system. Command used: python3 01_build_database.py -c 04_TransportTools/hEpx_E470G_tt.ini -o hEpx_E470G.dat