cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7966540
title: MD trajectories for "Kinetic barrier to enzyme inhibition is manipulated by dynamical local interactions in E. coli DHFR"

description: Dihydrofolate reductase (DHFR) is an important drug target and a highly studied model<br> protein for understanding enzyme dynamics. DHFR’s crucial role in folate synthesis renders it<br> an ideal candidate to understand protein function and protein evolution mechanisms. In this<br> study, to understand how a newly proposed DHFR inhibitor, 4’-deoxy methyl trimethoprim<br> (4’-DTMP), alters evolutionary trajectories, we studied interactions that lead to its superior<br> performance over trimethoprim (TMP). To elucidate the inhibition mechanism of 4’-DTMP,<br> we first confirmed, both computationally and experimentally, that the relative binding free<br> energy cost for the mutation of TMP and 4’-DTMP are the same, pointing to the origin of the<br> characteristic differences to be kinetic rather than thermodynamic. We then employed an<br> interaction-based analysis by focusing first on the active site, then on the whole enzyme. We<br> confirmed that the polar modification in 4’-DTMP induces additional local interactions with<br> the enzyme, particularly the M20 loop. These changes are propagated to the whole enzyme as<br> shifts in the hydrogen bond networks. To shed light on the allosteric interactions, we support<br> our analysis with network-based community analysis and show that segmentation of the loop<br> domain of the inhibitor-bound DHFR must be avoided by a successful inhibitor.
description: for analyses of the trajectories you can visit the GitHub page: https://github.com/midstlab/JCIM_Cetin_etal_2023 Dataset 1: tmpp-WT-1.dcd, tmpp-WT-2.dcd, tmpp-WT-3.dcd, tmpp-WT-4.dcd, tmpp-WT-5.dcd, corresponding psf file : tmpp-WT-pro.psf tmpp-L28R-1.dcd, tmpp-L28R-2.dcd, tmpp-L28R-3.dcd, tmpp-L28R-4.dcd, tmpp-L28R-5.dcd, corresponding psf file : tmpp-L28R-pro.psf d4tmpp-WT-1.dcd, d4tmpp-WT-2.dcd, d4tmpp-WT-3.dcd, d4tmpp-WT-4.dcd, d4tmpp-WT-5.dcd, corresponding psf file : d4tmpp-WT-pro.psf d4tmpp-L28R-1.dcd, d4tmpp-L28R-2.dcd, d4tmpp-L28R-3.dcd, d4tmpp-L28R-4.dcd, d4tmpp-L28R-5.dcd, corresponding psf file : d4tmpp-L28R-pro.psf protein-only, stride 100, 1 microsecond chopped into five. Dataset 2: tmpp-WT.dcd, tmpp-L28R.dcd, d4tmpp-WT.dcd, d4tmpp-L28R.dcd all atoms, stride 500, 1 microsecond each
DOI: 10.5281/zenodo.7966539
title: MD trajectories for "Kinetic barrier to enzyme inhibition is manipulated by dynamical local interactions in E. coli DHFR"

description: Dihydrofolate reductase (DHFR) is an important drug target and a highly studied model<br> protein for understanding enzyme dynamics. DHFR’s crucial role in folate synthesis renders it<br> an ideal candidate to understand protein function and protein evolution mechanisms. In this<br> study, to understand how a newly proposed DHFR inhibitor, 4’-deoxy methyl trimethoprim<br> (4’-DTMP), alters evolutionary trajectories, we studied interactions that lead to its superior<br> performance over trimethoprim (TMP). To elucidate the inhibition mechanism of 4’-DTMP,<br> we first confirmed, both computationally and experimentally, that the relative binding free<br> energy cost for the mutation of TMP and 4’-DTMP are the same, pointing to the origin of the<br> characteristic differences to be kinetic rather than thermodynamic. We then employed an<br> interaction-based analysis by focusing first on the active site, then on the whole enzyme. We<br> confirmed that the polar modification in 4’-DTMP induces additional local interactions with<br> the enzyme, particularly the M20 loop. These changes are propagated to the whole enzyme as<br> shifts in the hydrogen bond networks. To shed light on the allosteric interactions, we support<br> our analysis with network-based community analysis and show that segmentation of the loop<br> domain of the inhibitor-bound DHFR must be avoided by a successful inhibitor.
description: for analyses of the trajectories you can visit the GitHub page: https://github.com/midstlab/JCIM_Cetin_etal_2023 Dataset 1: tmpp-WT-1.dcd, tmpp-WT-2.dcd, tmpp-WT-3.dcd, tmpp-WT-4.dcd, tmpp-WT-5.dcd, corresponding psf file : tmpp-WT-pro.psf tmpp-L28R-1.dcd, tmpp-L28R-2.dcd, tmpp-L28R-3.dcd, tmpp-L28R-4.dcd, tmpp-L28R-5.dcd, corresponding psf file : tmpp-L28R-pro.psf d4tmpp-WT-1.dcd, d4tmpp-WT-2.dcd, d4tmpp-WT-3.dcd, d4tmpp-WT-4.dcd, d4tmpp-WT-5.dcd, corresponding psf file : d4tmpp-WT-pro.psf d4tmpp-L28R-1.dcd, d4tmpp-L28R-2.dcd, d4tmpp-L28R-3.dcd, d4tmpp-L28R-4.dcd, d4tmpp-L28R-5.dcd, corresponding psf file : d4tmpp-L28R-pro.psf protein-only, stride 100, 1 microsecond chopped into five. Dataset 2: tmpp-WT.dcd, tmpp-L28R.dcd, d4tmpp-WT.dcd, d4tmpp-L28R.dcd all atoms, stride 500, 1 microsecond each
DOI: 10.34740/kaggle/dsv/5805511
title: COVID Vaccination in World (updated daily)
DOI: 10.5281/zenodo.7981760
title: 32 Water molecule simulation

description: This is a microcanonical ensemble (NVE) simulation of 32 water molecules at a temperature<br> of 300 K, approximated with the Lennard-Jones force-field, using cp2k. The physical simulation is done employing a step-size of 0.1 fs for 100,000 steps. The simulation is done without periodic spatial boundaries in order to have a<br> system that fundamentally evolves over time.
DOI: 10.5281/zenodo.7981759
title: 32 Water molecule simulation

description: This is a microcanonical ensemble (NVE) simulation of 32 water molecules at a temperature<br> of 300 K, approximated with the Lennard-Jones force-field, using cp2k. The physical simulation is done employing a step-size of 0.1 fs for 100,000 steps. The simulation is done without periodic spatial boundaries in order to have a<br> system that fundamentally evolves over time.
DOI: 10.5517/ccdc.csd.cc27pjcv
title: CCDC 2076267: Experimental Crystal Structure Determination

description: Related Article: Jian-Hong Tang, Hao Li, Chaonan Yuan, Giacomo Parigi, Claudio Luchinat, Thomas J. Meade|2023|J.Am.Chem.Soc.|145|10045|doi:10.1021/jacs.2c13672
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.cc2dhtg6
title: CCDC 2219738: Experimental Crystal Structure Determination

description: Related Article: Edwin R. Sukandar, Sutin Kaennakam, Sutthida Wongsuwan, Jaruwan Chatwichien, Sucheewin Krobthong, Yodying Yingchutrakul, Thanisorn Mahatnirunkul, Fadjar Mulya, Vudhichai Parasuk, David J. Harding, Preeyaporn Poldorn, Thanyada Rungrotmongkol, Santi Tip-pyang, Chanat Aonbangkhen, Warinthorn Chavasiri|2023|Phytochemistry|211|113701|doi:10.1016/j.phytochem.2023.113701
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.cc2dhth7
title: CCDC 2219739: Experimental Crystal Structure Determination

description: Related Article: Edwin R. Sukandar, Sutin Kaennakam, Sutthida Wongsuwan, Jaruwan Chatwichien, Sucheewin Krobthong, Yodying Yingchutrakul, Thanisorn Mahatnirunkul, Fadjar Mulya, Vudhichai Parasuk, David J. Harding, Preeyaporn Poldorn, Thanyada Rungrotmongkol, Santi Tip-pyang, Chanat Aonbangkhen, Warinthorn Chavasiri|2023|Phytochemistry|211|113701|doi:10.1016/j.phytochem.2023.113701
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.cc2dr8zf
title: CCDC 2226915: Experimental Crystal Structure Determination

description: Related Article: Valentin Vaillant-Coindard, Florian Chotard, Benjamin Théron, Cédric Balan, Jérôme Bayardon, Raluca Malacea-Kabbara, Ewen Bodio, Yoann Rousselin, Paul Fleurat-Lessard, Pierre Le Gendre|2023|Inorg.Chem.|62|7342|doi:10.1021/acs.inorgchem.3c00493
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.cc2dr90h
title: CCDC 2226916: Experimental Crystal Structure Determination

description: Related Article: Valentin Vaillant-Coindard, Florian Chotard, Benjamin Théron, Cédric Balan, Jérôme Bayardon, Raluca Malacea-Kabbara, Ewen Bodio, Yoann Rousselin, Paul Fleurat-Lessard, Pierre Le Gendre|2023|Inorg.Chem.|62|7342|doi:10.1021/acs.inorgchem.3c00493
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.cc2dr91j
title: CCDC 2226917: Experimental Crystal Structure Determination

description: Related Article: Valentin Vaillant-Coindard, Florian Chotard, Benjamin Théron, Cédric Balan, Jérôme Bayardon, Raluca Malacea-Kabbara, Ewen Bodio, Yoann Rousselin, Paul Fleurat-Lessard, Pierre Le Gendre|2023|Inorg.Chem.|62|7342|doi:10.1021/acs.inorgchem.3c00493
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.cc2dr92k
title: CCDC 2226918: Experimental Crystal Structure Determination

description: Related Article: Valentin Vaillant-Coindard, Florian Chotard, Benjamin Théron, Cédric Balan, Jérôme Bayardon, Raluca Malacea-Kabbara, Ewen Bodio, Yoann Rousselin, Paul Fleurat-Lessard, Pierre Le Gendre|2023|Inorg.Chem.|62|7342|doi:10.1021/acs.inorgchem.3c00493
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.cc2dr93l
title: CCDC 2226919: Experimental Crystal Structure Determination

description: Related Article: Valentin Vaillant-Coindard, Florian Chotard, Benjamin Théron, Cédric Balan, Jérôme Bayardon, Raluca Malacea-Kabbara, Ewen Bodio, Yoann Rousselin, Paul Fleurat-Lessard, Pierre Le Gendre|2023|Inorg.Chem.|62|7342|doi:10.1021/acs.inorgchem.3c00493
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.cc2dr94m
title: CCDC 2226920: Experimental Crystal Structure Determination

description: Related Article: Valentin Vaillant-Coindard, Florian Chotard, Benjamin Théron, Cédric Balan, Jérôme Bayardon, Raluca Malacea-Kabbara, Ewen Bodio, Yoann Rousselin, Paul Fleurat-Lessard, Pierre Le Gendre|2023|Inorg.Chem.|62|7342|doi:10.1021/acs.inorgchem.3c00493
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.cc2dr95n
title: CCDC 2226921: Experimental Crystal Structure Determination

description: Related Article: Valentin Vaillant-Coindard, Florian Chotard, Benjamin Théron, Cédric Balan, Jérôme Bayardon, Raluca Malacea-Kabbara, Ewen Bodio, Yoann Rousselin, Paul Fleurat-Lessard, Pierre Le Gendre|2023|Inorg.Chem.|62|7342|doi:10.1021/acs.inorgchem.3c00493
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.cc2dr96p
title: CCDC 2226922: Experimental Crystal Structure Determination

description: Related Article: Valentin Vaillant-Coindard, Florian Chotard, Benjamin Théron, Cédric Balan, Jérôme Bayardon, Raluca Malacea-Kabbara, Ewen Bodio, Yoann Rousselin, Paul Fleurat-Lessard, Pierre Le Gendre|2023|Inorg.Chem.|62|7342|doi:10.1021/acs.inorgchem.3c00493
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.cc2f1rw4
title: CCDC 2236026: Experimental Crystal Structure Determination

description: Related Article: Shuaixin Fan, Weiping Wu, Lili Fang, Jin Zhu|2023|Org.Lett.|25|3335|doi:10.1021/acs.orglett.3c01249
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.cc2f4bvs
title: CCDC 2238505: Experimental Crystal Structure Determination

description: Related Article: Shulin Jiao, Zheng Tang, Dong Li, Cuiping Xu, Zhu Yang, Peng Chen, Xiaofan Sun, Hong-Ling Cai, Xiaoshan Wu|2023|Chem.Eng.Journal|466|143188|doi:10.1016/j.cej.2023.143188
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.cc2f73wp
title: CCDC 2241172: Experimental Crystal Structure Determination

description: Related Article: Cristina Negro, Sergio Sanz-Navarro, Antonio Leyva-Pérez, Donatella Armentano, Jesús Ferrando-Soria, Emilio Pardo|2023|Inorg.Chem.|62|7353|doi:10.1021/acs.inorgchem.3c00495
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.7981210
title: ConfFix dataset

description: ConfFix Dataset Please find <code>Section_3.xlsx</code> for the detailed information of our empirical study in Section 3. The dataset for evaluating ConfFix contains 81 reproducible CC issues. Please check <code>issue_in_the_latest_version.xlsx</code> and <code>issue_in_the_past.xlsx</code> for the information of 77 CC issues, including the reproduction videos and our submitted pull requests and <strong>issue reports</strong> to the app developers. For the detail please check <code>issue_in_the_latest_version.xlsx</code>. The APK files of these 77 CC issues are provided in <code>subject_apks.zip</code> folder when you run the experiment. Please refer to <code>list_sh.xlsx</code> to find the commands for the experiments. We also release the experimental results of ConfFix, XFix and Lint in <code>Lint&ConfFix&XFix output.xlsx</code>. Besides, the raw outputs of ConfFix and XFix can be found in <code>conffix-output.zip</code> and <code>xfix-output.zip</code> folders.
DOI: 10.5281/zenodo.7981209
title: ConfFix dataset

description: ConfFix Dataset Please find <code>Section_3.xlsx</code> for the detailed information of our empirical study in Section 3. The dataset for evaluating ConfFix contains 81 reproducible CC issues. Please check <code>issue_in_the_latest_version.xlsx</code> and <code>issue_in_the_past.xlsx</code> for the information of 77 CC issues, including the reproduction videos and our submitted pull requests and <strong>issue reports</strong> to the app developers. For the detail please check <code>issue_in_the_latest_version.xlsx</code>. The APK files of these 77 CC issues are provided in <code>subject_apks.zip</code> folder when you run the experiment. Please refer to <code>list_sh.xlsx</code> to find the commands for the experiments. We also release the experimental results of ConfFix, XFix and Lint in <code>Lint&ConfFix&XFix output.xlsx</code>. Besides, the raw outputs of ConfFix and XFix can be found in <code>conffix-output.zip</code> and <code>xfix-output.zip</code> folders.
DOI: 10.6084/m9.figshare.23257091
title: Shal ewes (B-2)

description: ovary tissue of shal ewes , RNA-SEQ from ovarian IRAN Breed
DOI: 10.6084/m9.figshare.23257091.v1
title: Shal ewes (B-2)

description: ovary tissue of shal ewes , RNA-SEQ from ovarian IRAN Breed
DOI: 10.5281/zenodo.7982000
title: Non-identical moire twins in bilayer graphene revealed by valley Hall effect measurements

description: The superlattice obtained by aligning a monolayer graphene and boron nitride (BN) inherits from the hexagonal lattice a sixty degrees periodicity with the layer alignment. It implies that, in principle, the properties of the heterostructure must be identical for 0$^{\circ}$ and 60$^{\circ}$ of layer alignment. Here, we demonstrate, using dynamically rotatable van der Waals heterostructures, that the moir\'e superlattice formed in a bilayer graphene/BN has different electronic properties at 0$^{\circ}$ and 60$^{\circ}$ of alignment. Although the existence of these non-identical moir\'e twins is explained by different relaxation of the atomic structures for each alignment, the origin of the observed valley Hall effect remains to be explained. A simple Berry curvature argument do not hold to explain the hundred and twenty degrees periodicity of this observation. Our results highlight the complexity of the interplay between mechanical and electronic properties on moir\'e structure and the importance of taking into account atomic structure relaxation to understand its electronic properties.
DOI: 10.5281/zenodo.7981999
title: Non-identical moire twins in bilayer graphene revealed by valley Hall effect measurements

description: The superlattice obtained by aligning a monolayer graphene and boron nitride (BN) inherits from the hexagonal lattice a sixty degrees periodicity with the layer alignment. It implies that, in principle, the properties of the heterostructure must be identical for 0$^{\circ}$ and 60$^{\circ}$ of layer alignment. Here, we demonstrate, using dynamically rotatable van der Waals heterostructures, that the moir\'e superlattice formed in a bilayer graphene/BN has different electronic properties at 0$^{\circ}$ and 60$^{\circ}$ of alignment. Although the existence of these non-identical moir\'e twins is explained by different relaxation of the atomic structures for each alignment, the origin of the observed valley Hall effect remains to be explained. A simple Berry curvature argument do not hold to explain the hundred and twenty degrees periodicity of this observation. Our results highlight the complexity of the interplay between mechanical and electronic properties on moir\'e structure and the importance of taking into account atomic structure relaxation to understand its electronic properties.
DOI: 10.5281/zenodo.7982070
title: Pollino seismic waveforms

description: The repository contains all the waveforms used to perform 3D scattering and absorption imaging of the Pollino seismic gap area.
DOI: 10.5281/zenodo.7982069
title: Pollino seismic waveforms

description: The repository contains all the waveforms used to perform 3D scattering and absorption imaging of the Pollino seismic gap area.
DOI: 10.17028/rd.lboro.23257256
title: Supplementary information files for Attending sporting mega events during COVID-19: mitigation and messaging at UK EURO 2020 matches

description: Supplementary files for article Attending sporting mega events during COVID-19: mitigation and messaging at UK EURO 2020 matches The UEFA EURO 2020 football tournament was one of the largest Sporting Mega Events (SMEs) to take place during the COVID-19 pandemic. Mitigating the risk of virus transmission requires a multi-layered approach for any large event, more so in this case due to staging the tournament across eleven host countries. Yet, little is known about COVID-19 risks and mitigation from attending an event of this scale and nature. We examined the implementation of mitigation and messaging at EURO 2020 matches hosted at venues in the UK. The tournament was postponed from the summer of 2020 and played in June and July of 2021. Structured observations were conducted by 11 trained fieldwork-supporters at 10 matches played at Wembley Stadium, London, or Hampden Park, Glasgow. Fieldwork-supporters observed one-way systems and signage, and hand sanitizing stations inside the stadia, but reported significant variation in the implementation of staggered timeslots, testing upon entry, and procedures for exit. Adherence to planned measures by ticket holders and implementation by stewards waned as the tournament progressed culminating in an absence of enforced measures at the final. The non-compliance with COVID-19 mitigation measures was likely to have led to a significantly increased risk of transmission. Future events should consider how COVID-19 mitigation measures could become 'new norms' of fan behaviour, learning from what is already known about football fandom. Tournament organizers of SMEs can use these findings to promote clearer messaging on pandemic-driven changes in fan behaviour and best practices in mitigating risk at future sporting and cultural events. <br>