DOI: 10.5281/zenodo.11092891
title: Reinforcing Tunnel Network Exploration in Proteins using Gaussian Accelerated Molecular Dynamics (inputs, outputs, analysis)

description: 00_LinB-Wt.tar.gz - LinB-Wt: contains raw data that are used for analysis, also conatin folder for GaMD testing.


    1. cMD(Classical MD simulation) analysis files :            1. Analysis of catalytic residue’s RMSD, whole protein RMSD and RMSF along with whole protein’s Rg and sasa.        2. Inputs and output files of caver calculations.         3. H-bond raw distance files from all simulations named run1-run5.         4. Distance files used to calculate PCA and cluster analysis.        5. Input files and input structure used to run simulations along with output restart files from each stage of production.           2. GaMD(Gaussian Accelerated MD simulation) analysis files :          1. Analysis of catalytic residue’s RMSD, whole protein RMSD and RMSF along with whole protein’s Rg and sasa.        2. Inputs and output files of caver calculations.         3. H-bond raw distance files from all simulations named run1-run5.         4. Distance files used to calculate PCA and cluster analysis.        5. Input files and input structure used to run simulations along with output restart files from each stage of production.

    3. GaMD-testing :

        1. Input file of GaMD used to run testing and output gamd.log files for multiple run of σOP 1.2 - 1.4 and σOD 2.5.

    4. Initial 200ns cMD simulation files used for cluster analysis :

        1. Force field parameters and input coordinates *.inpcrd, parameters *.parm7 and 200ns stripped water and ions simulation in Amber *.nc format        2. Restart files for each stage of the minimization, equilibration and production runs in Amber *.rst format in rst folder.        3. Ouput files from Simulation for each stage of the minimization, equilibration and production runs in Amber *.out format in out folder.



01_LinB-Open.tar.gz - LinB Open mutant: contains raw data that are used for analysis.


    1. cMD(Classical MD simulation) analysis files :            1. Analysis of catalytic residue’s RMSD, whole protein RMSD and RMSF along with whole protein’s Rg and sasa.        2. Inputs and output files of caver calculations.         3. H-bond raw distance files from all simulations named run1-run5.         4. Distance files used to calculate PCA and cluster analysis.        5. Input files and input structure used to run simulations along with output restart files from each stage of production.           2. GaMD(Gaussian Accelerated MD simulation) analysis files :          1. Analysis of catalytic residue’s RMSD, whole protein RMSD and RMSF along with whole protein’s Rg and sasa.        2. Inputs and output files of caver calculations.         3. H-bond raw distance files from all simulations named run1-run5.         4. Distance files used to calculate PCA and cluster analysis.        5. Input files and input structure used to run simulations along with output restart files from each stage of production.

    3. Initial 200ns cMD simulation files used for cluster analysis :

        1. Force field parameters and input coordinates *.inpcrd, parameters *.parm7 and 200ns stripped water and ions simulation in Amber *.nc format        2. Restart files for each stage of the minimization, equilibration and production runs in Amber *.rst format in rst folder.        3. Ouput files from Simulation for each stage of the minimization, equilibration and production runs in Amber *.out format in out folder.



02_LinB-Closed.tar.gz - LinB Closed mutant: contains raw data that are used for analysis.


    1. cMD(Classical MD simulation) analysis files :            1. Analysis of catalytic residue’s RMSD, whole protein RMSD and RMSF along with whole protein’s Rg and sasa.        2. Inputs and output files of caver calculations.         3. H-bond raw distance files from all simulations named run1-run5.         4. Distance files used to calculate PCA and cluster analysis.        5. Input files and input structure used to run simulations along with output restart files from each stage of production.           2. GaMD(Gaussian Accelerated MD simulation) analysis files :          1. Analysis of catalytic residue’s RMSD, whole protein RMSD and RMSF along with whole protein’s Rg and sasa.        2. Inputs and output files of caver calculations.         3. H-bond raw distance files from all simulations named run1-run5.         4. Distance files used to calculate PCA and cluster analysis.        5. Input files and input structure used to run simulations along with output restart files from each stage of production.

    3. Initial 200ns cMD simulation files used for cluster analysis :

        1. Force field parameters and input coordinates *.inpcrd, parameters *.parm7 and 200ns stripped water and ions simulation in Amber *.nc format        2. Restart files for each stage of the minimization, equilibration and production runs in Amber *.rst format in rst folder.        3. Ouput files from Simulation for each stage of the minimization, equilibration and production runs in Amber *.out format in out folder.



03_TT_analysis.tar.gz - TransportTools: contains config file and all the raw data from all set and subset of reclustered (using in-house python script) caver calculations used for running TT.


    1. Caver input data for comparison between 500ns, 1 us, 2.5 us and 5us between LinB-Wt and it’s mutants.    2. TransportTools log file.    3. Main statistics result of comparative analysis.



04_reweighting.tar.gz: directory contains reweighted .csv files after running in-house reweighting protocol.           1. GaMD log files from each simulation of LinB-Wt and it’s mutants.    2. CSV files from TT result folder.    3. Result *.csv file contained reweighted tunnel properties in folder reweighted_filtered_new.

05_caverdock.tar.gz: contains raw data for caverdock calculations uisng 100 best tunnels with four ligands 2-bromoethanol (be), 1,2-dibromoethane (dbe), Bromide ion (br-) and water (h2o).


    1. Top 100 tunnels present in tunnel folder for all three tunnels ST, p1b and p3 with subdirectory containing three variants and four ligand, whichare used for running caverdock.    2. Ligand *.pdbqt file and receptor *.pdbqt are present in each 100 tunnel folder of respective caverdock calculation.    3. Inside each variant and each ligand, there is respective result of migration analysis with energy barrier calculation of respective tunnels *energy_barriers-new.log* and further simplied *.csv files that was used for preparing figure in manuscript.

 
description: This work was supported by the National Science Centre, Poland (Grant Number 2017/26/E/NZ1/00548). The computations were performed at the Poznan Supercomputing and Networking Center.