Water will find its way: transport through narrow tunnels in hydrolases (Epx protein)

Water will find its way: transport through narrow tunnels in hydrolases (Epx protein)

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

1. 01_Simulations.tar.gz: All the files used to get the data employing Molecular Dynamics simulations.
2. 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.
3. 03_Aquaduct.tar.gz: Aquaduct results for all the MD trajectories.
4. 04_TransportTools.tar.gz: TransportTools results (https://doi.org/10.1093/bioinformatics/btab872).
5. 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 and contact analyses are here.

Files

1. 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.
2. Epx.dat Parsed database of transport events for Epx system. Command used: python3 01_build_database.py -c 04_TransportTools/Epx_tt.ini -o Epx.dat