DOI: 10.5281/zenodo.16874308
title: Unlocking high-throughput investigation of transport tunnels in enzymes using coarse-grained simulation methods

description: (00_AA.tar.gz) All-Atom (AA) files: contains raw data that are used for analysis and also contain a folder for the initial cMD simulation file for cluster analysis to generate starting structures that were used to run all LinB simulations using different methods.

    1. LinB-Wt analysis files :

                1. Analysis folder contains raw data for whole protein RMSD and RMSF along with whole protein’s Rg and sasa, additional pentad residues rmsd.                2. Output files of caver divide-n-conquer calculations.                 3. Input files and input structure used to run simulations along with output restart files from each stage of production.           2. LinB-Closed analysis files : 

                1. Analysis folder conatin raw data for whole protein RMSD and RMSF along with whole protein’s Rg and sasa.                2. Output files of caver divide-n-conquer calculations.                3. Input files and input structure used to run simulations along with output restart files from each stage of production.

    3. LinB-Open analysis files :

                1. Analysis folder contains whole protein RMSD and RMSF along with whole protein’s Rg and sasa.                2. Output files of caver divide-n-conquer calculations.                3. Input files and input structure used to run simulations along with output restart files from each stage of production.

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

                1. Force field parameters and input coordinates *.inpcrd, parameters *.parm7.                2. Restart files for each stage of the minimization, equilibration and production runs in Amber *.rst format in rst folder.                3. Output files from simulation for each stage of the minimization, equilibration, and production runs in Amber *.out format in out folder.

(01_Elastic.tar.gz) Elastic Coarse Grained (CG): contains raw data of CG Martini Elastic simulations that are used for analysis.

    1. LinB-Wt analysis files :

                1. Whole protein RMSD and RMSF along with whole protein’s Rg and sasa, additional pentad residues rmsd.                2. Output files of caver divide and conquer calculations.                3. Input files used to run simulations along with output restart files from each stage of production.

    2. LinB-Closed analysis files :

                1. Whole protein RMSD and RMSF along with whole protein’s Rg and sasa.                2. Output files of caver divide and conquer calculations.                3. Input files used to run simulations along with output restart files from each stage of production.

    3. LinB-Open analysis files :

                1. Whole protein RMSD and RMSF along with whole protein’s Rg and sasa.                2. Output files of caver divide and conquer calculations.                3. Input files used to run simulations along with output restart files from each stage of production.

(02_Go.tar.gz) GO CG: contains raw data of CG Martini Go simulations that are used for analysis.

    1. LinB-Wt analysis files :

                1. Whole protein RMSD and RMSF along with whole protein’s Rg and sasa, additional pentad residues rmsd.                2. Output files of caver divide and conquer calculations.                3. Input files used to run simulations along with output restart files from each stage of production.

    2. LinB-Closed analysis files :

                1. Whole protein RMSD and RMSF along with whole protein’s Rg and sasa.                2. Output files of caver divide and conquer calculations.                3. Input files used to run simulations along with output restart files from each stage of production.

    3. LinB-Open analysis files :

                1. Whole protein RMSD and RMSF along with whole protein’s Rg and sasa.                2. Output files of caver divide and conquer calculations.                3. Input files used to run simulations along with output restart files from each stage of production.

(03_Sirah.tar.gz)  Sirah CG: contains raw data of CG Sirah simulations that are used for analysis.

    1. LinB-Wt analysis files :

                1. Whole protein RMSD and RMSF along with whole protein’s Rg and sasa, additional pentad residues rmsd.                2. Output files of caver divide and conquer calculations.                3. Input files used to run simulations along with output restart files from each stage of production.

    2. LinB-Closed analysis files :

                1. Whole protein RMSD and RMSF along with whole protein’s Rg and sasa.                2. Output files of caver divide and conquer calculations.                3. Input files used to run simulations along with output restart files from each stage of production.

    3. LinB-Open analysis files :

                1. Whole protein RMSD and RMSF along with whole protein’s Rg and sasa.                2. Output files of caver divide and conquer calculations.                3. Input files used to run simulations along with output restart files from each stage of production.

(04_TT_analysis.tar.gz): Transport Tools comparative analysis with AA, elastic CG model, go CG model and sirah CG simulations of 5 replicas from LinB-Wt, LinB-Closed and LinB-Open.

                1. TransportTools log file.                2. CSV files from TT result folder in supercluster folder placed inside data folder.                3. Bottleneck residues information in superclusters folder placed in data folder.                3. Main statistics result of comparative analysis.

(05_EC_class1-3.tar.gz): contains data for 9 enzymes from EC1-3 classes.

                1. Three enzymes from EC1 class calculated using AA, elastic CG model, go CG model and sirah CG, their rmsf and rmsf are included in analysis folder.                2. Input files and output restart files and production *.log file.                3. Transport Tools result files - statistic file for comparative analysis among different methods, config file. *correlation.txt file used for calculating correlation analysis and TransportTools log file.

(06_TT_backmap.tar.gz): contains config file for Transport Tools and all the results from the elastic coarse grained model, elastic backmap and all-atom structures for LinB-Wt.

                1. TransportTools log file.                2. Main statistics result of comparative analysis.                3. CSV files from TT results in supercluster folder placed inside data folder.

               
description: This work was supported by the National Science Centre, Poland (grant nos. 2023/49/N/NZ2/02567 to N.M. and 2017/26/E/NZ1/00548 to J.B.). Computations by N.M. and J.B. were performed at the Poznan Supercomputing and Networking Center.