DOI: 10.5281/zenodo.10911961
title: Water will find its way: transport through narrow tunnels in hydrolases (Hal protein with different MD simulation settings)

description: Hal_2fs.zip

"Water will find a way: transport through narrow tunnels in hydrolases (Hal_2fs protein variant)"

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 folders depending the stage they belong to.

Folders

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 analysis 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. Hal_2fs.dat: Parsed database of transport events for Hal system. Command used: python3 01_build_database.py -c 04_TransportTools/Hal_2fs.ini -o Hal_2fs.dat

 

Hal_300K.zip

"Water will find a way: transport through narrow tunnels in hydrolases (Hal_300K protein variant)"

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 folders depending the stage they belong to.

Folders

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 analysis 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. Hal_300K.dat: Parsed database of transport events for Hal system. Command used:python3 01_build_database.py -c 04_TransportTools/Hal_300K.ini -o Hal_300K.dat

 

Hal_TIP3P.zip

"Water will find a way: transport through narrow tunnels in hydrolases (TIP3P protein variant)"

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 folders depending the stage they belong to.

Folders

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 analysis 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. Hal_TIP3P.dat: Parsed database of transport events for Hal system. Command used:python3 01_build_database.py -c 04_TransportTools/Hal_TIP3P.ini -o Hal_TIP3P.dat
description: This work was supported by the National Science Centre, Poland (grant no. 2017/26/E/NZ1/00548). The computations were performed at the Poznan Supercomputing and Networking Center. C.S-B. and A.S.T. are recipients of a scholarship associated with the POWER project (grant nos. POWR.03.02.00-00-I022/16 and POWR.03.02.00-00-I006/17, respectively).