cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7966082
title: Water will find a way: transport through narrow tunnels in hydrolases (Hal protein)

description: <strong>Water will find a way: transport through narrow tunnels in hydrolases (Hal protein)</strong> <br> The input files and results used for the paper “<em>Water will find a way: transport through narrow tunnels in hydrolases</em>” are separated in the different folders depending the stage they belong to. <strong>01_Simulations.tar.gz:</strong> All the files used to get the data employing Molecular Dynamics simulations. <strong>02_Caver.tar.gz:</strong> 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. <strong>03_Aquaduct.tar.gz:</strong> Aquaduct results for all the MD trajectories. <strong>04_TransportTools.tar.gz:</strong> TransportTools results (https://doi.org/10.1093/bioinformatics/btab872). <strong>05_WaterAnalysis.tar.gz:</strong> 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. <strong>Files</strong> <strong>01_build_database.py</strong> 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. <strong>Hal.dat</strong> Parsed database of transport events for Hal system. Command used: <em>python3 01_build_database.py -c 04_TransportTools/Hal_tt.ini -o Hal.dat</em>
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). This repository is part of the paper "Water will find a way: transport through narrow tunnels in hydrolases", and the other repositories associated to it are Epx (10.5281/zenodo.7966059), hEpx (10.5281/zenodo.7965661), Lip (10.5281/zenodo.7966092) and E470G (10.5281/zenodo.7965881)
DOI: 10.5281/zenodo.10500990
title: Water will find its way: transport through narrow tunnels in hydrolases (E470G protein)

description: Water will find its way: transport through narrow tunnels in hydrolases (E470G 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 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: We employed the comparative approach to analyze the results with TransportTools (https://doi.org/10.1093/bioinformatics/btab872). Please see the README file inside for more explanations. Results can be found at Zenodo repository https://doi.org/10.5281/zenodo.7965661

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.
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). This repository is part of the paper "Water will find its way: transport through narrow tunnels in hydrolases", and the other repositories associated to it are Hal (10.5281/zenodo.7966082), Epx (10.5281/zenodo.7966059), Lip (10.5281/zenodo.7966092) and hEpx (10.5281/zenodo.7965661)
DOI: 10.5281/zenodo.7965661
title: Water will find a way: transport through narrow tunnels in hydrolases (hEpx protein)

description: <strong>Water will find a way: transport through narrow tunnels in hydrolases (hEpx protein)</strong> The input files and results used for the paper "<em>Water will find a way: transport through narrow tunnels in hydrolases</em>" are separated in the different files depending the stage they belong to. <strong>01_Simulations.tar.gz:</strong> All the files used to get the data employing Molecular Dynamics simulations. <strong>02_Caver.tar.gz:</strong> Caver config used together with the "<em>Divide-and-conquer approach to study protein tunnels in long molecular dynamics simulations"</em> method (https://doi.org/10.1016/j.mex.2022.101968), and after re-clustering as described in the methods section of the paper. <strong>03_Aquaduct.tar.gz:</strong> Aquaduct results for all the MD trajectories. <strong>04_TransportTools.tar.gz:</strong> 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). <strong>05_WaterAnalysis.tar.gz:</strong> 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. <strong>Files</strong> <strong>01_build_database.py</strong> 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. <strong>hEpx_E470G.dat</strong> Parsed database of transport events for hEpx_E470G system. Command used: <em>python3 01_build_database.py -c 04_TransportTools/hEpx_E470G_tt.ini -o hEpx_E470G.dat</em>
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). This repository is part of the paper "Water will find a way: transport through narrow tunnels in hydrolases", and the other repositories associated to it are Hal (10.5281/zenodo.7966082), Epx (10.5281/zenodo.7966059), Lip (10.5281/zenodo.7966092) and E470G (10.5281/zenodo.7965881)
DOI: 10.5281/zenodo.7965880
title: Water will find its way: transport through narrow tunnels in hydrolases (E470G protein)

description: Water will find its way: transport through narrow tunnels in hydrolases (E470G 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 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: We employed the comparative approach to analyze the results with TransportTools (https://doi.org/10.1093/bioinformatics/btab872). Please see the README file inside for more explanations. Results can be found at Zenodo repository https://doi.org/10.5281/zenodo.7965661

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.
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). This repository is part of the paper "Water will find its way: transport through narrow tunnels in hydrolases", and the other repositories associated to it are Hal (10.5281/zenodo.7966082), Epx (10.5281/zenodo.7966059), Lip (10.5281/zenodo.7966092) and hEpx (10.5281/zenodo.7965661)
DOI: 10.5281/zenodo.7965881
title: Water will find a way: transport through narrow tunnels in hydrolases (E470G protein)

description: <strong>Water will find a way: transport through narrow tunnels in hydrolases (E470G protein)</strong> The input files and results used for the paper "<em>Water will find a way: transport through narrow tunnels in hydrolases</em>" are separated in the different files depending the stage they belong to. <strong>01_Simulations.tar.gz:</strong> All the files used to get the data employing Molecular Dynamics simulations. <strong>02_Caver.tar.gz:</strong> Caver config used together with the "<em>Divide-and-conquer approach to study protein tunnels in long molecular dynamics simulations"</em> method (https://doi.org/10.1016/j.mex.2022.101968), and after re-clustering as described in the methods section of the paper. <strong>03_Aquaduct.tar.gz:</strong> Aquaduct results for all the MD trajectories. <strong>04_TransportTools.tar.gz:</strong> We employed the comparative approach to analyze the results with TransportTools (https://doi.org/10.1093/bioinformatics/btab872). Please see the README file inside for more explanations. Results can be found at Zenodo repository https://doi.org/10.5281/zenodo.7965661 <strong>05_WaterAnalysis.tar.gz:</strong> 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. <strong>Files</strong> <strong>01_build_database.py</strong> 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. <strong>hEpx_E470G.dat</strong> Parsed database of transport events for hEpx_E470G system.
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). This repository is part of the paper "Water will find a way: transport through narrow tunnels in hydrolases", and the other repositories associated to it are Hal (10.5281/zenodo.7966082), Epx (10.5281/zenodo.7966059), Lip (10.5281/zenodo.7966092) and hEpx (10.5281/zenodo.7965661)
DOI: 10.5281/zenodo.7966092
title: Water will find a way: transport through narrow tunnels in hydrolases (Lip protein)

description: <strong>Water will find a way: transport through narrow tunnels in hydrolases (Lip protein)</strong> <br> The input files and results used for the paper “<em>Water will find a way: transport through narrow tunnels in hydrolases</em>” are separated in the different folders depending the stage they belong to. <strong>01_Simulations.tar.gz:</strong> All the files used to get the data employing Molecular Dynamics simulations. <strong>02_Caver.tar.gz:</strong> 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. <strong>03_Aquaduct.tar.gz:</strong> Aquaduct results for all the MD trajectories. <strong>04_TransportTools.tar.gz:</strong> TransportTools results (https://doi.org/10.1093/bioinformatics/btab872). <strong>05_WaterAnalysis.tar.gz:</strong> 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. <strong>Files</strong> <strong>01_build_database.py</strong> 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. <strong>Lip.dat</strong> Parsed database of transport events for Lip system. Command used: <em>python3 01_build_database.py -c 04_TransportTools/Lip_tt.ini -o Lip.dat</em>
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). This repository is part of the paper "Water will find a way: transport through narrow tunnels in hydrolases", and the other repositories associated to it are Hal (10.5281/zenodo.7966082), Epx (10.5281/zenodo.7966059), hEpx (10.5281/zenodo.7965661) and E470G (10.5281/zenodo.7965881)
DOI: 10.6084/m9.figshare.24994784
title: Results of the simulation - Protein Ligand Compex

description: .Gro file is the Gromacs structure file of the protein ligand complex after simulation and .xtc file is the trajectory file
DOI: 10.6084/m9.figshare.24994784.v1
title: Results of the simulation - Protein Ligand Compex

description: .Gro file is the Gromacs structure file of the protein ligand complex after simulation and .xtc file is the trajectory file
DOI: 10.6084/m9.figshare.24994790
title: Results of the simulation - protein without ligand

description: .gro file is the Gromacs structure file after the simulation and .xtc file is the trajectory file
DOI: 10.6084/m9.figshare.24994790.v1
title: Results of the simulation - protein without ligand

description: .gro file is the Gromacs structure file after the simulation and .xtc file is the trajectory file
DOI: 10.5517/ccdc.csd.cc2fbpk1
title: CCDC 2244603: Experimental Crystal Structure Determination

description: Related Article: Liam Grunwald, Mariko Inoue, Paula Cendoya Carril, Paula Cendoya Carril, Paula Cendoya Carril|2023|Chem (Cell Press)|10|365|doi:10.1016/j.chempr.2023.09.023
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2fbpl2
title: CCDC 2244604: Experimental Crystal Structure Determination

description: Related Article: Liam Grunwald, Mariko Inoue, Paula Cendoya Carril, Paula Cendoya Carril, Paula Cendoya Carril|2023|Chem (Cell Press)|10|365|doi:10.1016/j.chempr.2023.09.023
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2fbpn4
title: CCDC 2244606: Experimental Crystal Structure Determination

description: Related Article: Liam Grunwald, Mariko Inoue, Paula Cendoya Carril, Paula Cendoya Carril, Paula Cendoya Carril|2023|Chem (Cell Press)|10|365|doi:10.1016/j.chempr.2023.09.023
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2fbpq6
title: CCDC 2244608: Experimental Crystal Structure Determination

description: Related Article: Liam Grunwald, Mariko Inoue, Paula Cendoya Carril, Paula Cendoya Carril, Paula Cendoya Carril|2023|Chem (Cell Press)|10|365|doi:10.1016/j.chempr.2023.09.023
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2fbpm3
title: CCDC 2244605: Experimental Crystal Structure Determination

description: Related Article: Liam Grunwald, Mariko Inoue, Paula Cendoya Carril, Paula Cendoya Carril, Paula Cendoya Carril|2023|Chem (Cell Press)|10|365|doi:10.1016/j.chempr.2023.09.023
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2fbpp5
title: CCDC 2244607: Experimental Crystal Structure Determination

description: Related Article: Liam Grunwald, Mariko Inoue, Paula Cendoya Carril, Paula Cendoya Carril, Paula Cendoya Carril|2023|Chem (Cell Press)|10|365|doi:10.1016/j.chempr.2023.09.023
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.10501061
title: Projects' statistical information
DOI: 10.5281/zenodo.10501062
title: Projects' statistical information
DOI: 10.6084/m9.figshare.24994760
title: Metabolic Rate and Egg Production in Japanese Quails Can Be Predicted by Assessing Growth Parameters of Laying Hens

description: The aim of the current study was to assess the female metabolic rate and test the hypothesis that there is a relationship between the egg productivity of Japanese quails from eight breeds and their morphometric, or growth, parameters. Parameters measured were body weight (B), volume (V), and surface area (S), as well as the metabolism level expressed by the ratio S/V. The collected egg performance traits were as follows: the number of eggs produced (N), the average egg weight (W), and the total egg mass (M) (i.e., N multiplied by W). To measure the S and V values, a novel technique was developed that takes into account the similarity of the quail’s body to an ellipsoid. An analysis of the relationships between productivity indicators allowed us to introduce a new index called the metabolic index, B·S/V, based on all three main growth parameters in quails. Using the values of this index, we were then able to judge indirectly the level of quails’ egg productivity. We went on to assess the N, W, and M values, not only depending on the size of the bird’s growth parameters but also according to the degree of their changes during quail growth. These changes were expressed as the slope angles of trend lines describing the growth process data. This approach produced more accurate results for predicting the egg productivity in terms of W and M.
DOI: 10.6084/m9.figshare.24994769
title: Data file of the protein

description: Protein Databank File of KATG
DOI: 10.6084/m9.figshare.24994769.v1
title: Data file of the protein

description: Protein Databank File of KATG
DOI: 10.6084/m9.figshare.24994769.v2
title: Data file of the protein

description: Protein Databank File of KATG
DOI: 10.5281/zenodo.10501121
title: Analysis of maize growth under drought in an automated plant phenotyping platform

description: Supplemental data accompanying the PhD thesis of Lennart Verbraeken.
DOI: 10.5281/zenodo.8277978
title: Analysis of maize growth under drought in an automated plant phenotyping platform

description: Supplemental data accompanying the PhD thesis of Lennart Verbraeken.
DOI: 10.5281/zenodo.8277979
title: Analysis of maize growth under drought in an automated plant phenotyping platform

description: Supplemental data accompanying the PhD thesis of Lennart Verbraeken.
DOI: 10.34740/kaggle/dsv/7396510
title: ShxtsNGigs Podcast Youtube Performance
DOI: 10.5281/zenodo.10501138
title: Data set of the paper: Betrán, C. and Pons, M.A. (2022): "Stock Market Crises and Macroeconomic Depressions in Spain, 1850-2020". ODEON. 23, pp.179-202. ISSN: 1794-1113.
DOI: 10.5281/zenodo.10501139
title: Data set of the paper: Betrán, C. and Pons, M.A. (2022): "Stock Market Crises and Macroeconomic Depressions in Spain, 1850-2020". ODEON. 23, pp.179-202. ISSN: 1794-1113.
DOI: 10.6084/m9.figshare.24994856
title: Appendix C Contigs blasted results.pdfData for contigs blasted on NCBI generated from Ion Torrent NGS sequences through de novo assembly

description: Data for contigs blasted on NCBI generated from Ion Torrent NGS data assembly by de novo assembly to discover other viruses present in the sample and conducting further research through a viral metagenomic approach.
DOI: 10.6084/m9.figshare.24994856.v1
title: Appendix C Contigs blasted results.pdfData for contigs blasted on NCBI generated from Ion Torrent NGS sequences through de novo assembly

description: Data for contigs blasted on NCBI generated from Ion Torrent NGS data assembly by de novo assembly to discover other viruses present in the sample and conducting further research through a viral metagenomic approach.