cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13488881
title: 6lu7-0.pdb from Computational analysis of dynamic allostery and control in the SARS-CoV-2 main protease

description: The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has no publicly-available vaccine or antiviral drugs at the time of writing. An attractive coronavirus drug target is the main protease (M<sup>pro</sup>, also known as 3CL<sup>pro</sup>) because of its vital role in the viral cycle. A significant body of work has been focused on finding inhibitors which bind and block the active site of the main protease, but little has been done to address potential non-competitive inhibition, targeting regions other than the active site, partly because the fundamental biophysics of such allosteric control is still poorly understood. In this work, we construct an Elastic Network Model (ENM) of the SARS-CoV-2 M<sup>pro</sup> homodimer protein and analyse its dynamics and thermodynamics. We found a rich and heterogeneous dynamical structure, including allosterically correlated motions between the homodimeric protease's active sites. Exhaustive 1-point and 2-point mutation scans of the ENM and their effect on fluctuation free energies confirm previously experimentally identified bioactive residues, but also suggest several new candidate regions that are distant from the active site, yet control the protease function. Our results suggest new dynamically driven control regions as possible candidates for non-competitive inhibiting binding sites in the protease, which may assist the development of current fragment-based binding screens. The results also provide new insights into the active biophysical research field of protein fluctuation allostery and its underpinning dynamical structure.
DOI: 10.6084/m9.figshare.13488887
title: 6lu7-1point-25-K2K1.xlsx from Computational analysis of dynamic allostery and control in the SARS-CoV-2 main protease

description: The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has no publicly-available vaccine or antiviral drugs at the time of writing. An attractive coronavirus drug target is the main protease (M<sup>pro</sup>, also known as 3CL<sup>pro</sup>) because of its vital role in the viral cycle. A significant body of work has been focused on finding inhibitors which bind and block the active site of the main protease, but little has been done to address potential non-competitive inhibition, targeting regions other than the active site, partly because the fundamental biophysics of such allosteric control is still poorly understood. In this work, we construct an Elastic Network Model (ENM) of the SARS-CoV-2 M<sup>pro</sup> homodimer protein and analyse its dynamics and thermodynamics. We found a rich and heterogeneous dynamical structure, including allosterically correlated motions between the homodimeric protease's active sites. Exhaustive 1-point and 2-point mutation scans of the ENM and their effect on fluctuation free energies confirm previously experimentally identified bioactive residues, but also suggest several new candidate regions that are distant from the active site, yet control the protease function. Our results suggest new dynamically driven control regions as possible candidates for non-competitive inhibiting binding sites in the protease, which may assist the development of current fragment-based binding screens. The results also provide new insights into the active biophysical research field of protein fluctuation allostery and its underpinning dynamical structure.
DOI: 10.6084/m9.figshare.13488890.v1
title: 6lu7-croscor-25-2.xlsx from Computational analysis of dynamic allostery and control in the SARS-CoV-2 main protease

description: The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has no publicly-available vaccine or antiviral drugs at the time of writing. An attractive coronavirus drug target is the main protease (M<sup>pro</sup>, also known as 3CL<sup>pro</sup>) because of its vital role in the viral cycle. A significant body of work has been focused on finding inhibitors which bind and block the active site of the main protease, but little has been done to address potential non-competitive inhibition, targeting regions other than the active site, partly because the fundamental biophysics of such allosteric control is still poorly understood. In this work, we construct an Elastic Network Model (ENM) of the SARS-CoV-2 M<sup>pro</sup> homodimer protein and analyse its dynamics and thermodynamics. We found a rich and heterogeneous dynamical structure, including allosterically correlated motions between the homodimeric protease's active sites. Exhaustive 1-point and 2-point mutation scans of the ENM and their effect on fluctuation free energies confirm previously experimentally identified bioactive residues, but also suggest several new candidate regions that are distant from the active site, yet control the protease function. Our results suggest new dynamically driven control regions as possible candidates for non-competitive inhibiting binding sites in the protease, which may assist the development of current fragment-based binding screens. The results also provide new insights into the active biophysical research field of protein fluctuation allostery and its underpinning dynamical structure.
DOI: 10.6084/m9.figshare.13488887.v1
title: 6lu7-1point-25-K2K1.xlsx from Computational analysis of dynamic allostery and control in the SARS-CoV-2 main protease

description: The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has no publicly-available vaccine or antiviral drugs at the time of writing. An attractive coronavirus drug target is the main protease (M<sup>pro</sup>, also known as 3CL<sup>pro</sup>) because of its vital role in the viral cycle. A significant body of work has been focused on finding inhibitors which bind and block the active site of the main protease, but little has been done to address potential non-competitive inhibition, targeting regions other than the active site, partly because the fundamental biophysics of such allosteric control is still poorly understood. In this work, we construct an Elastic Network Model (ENM) of the SARS-CoV-2 M<sup>pro</sup> homodimer protein and analyse its dynamics and thermodynamics. We found a rich and heterogeneous dynamical structure, including allosterically correlated motions between the homodimeric protease's active sites. Exhaustive 1-point and 2-point mutation scans of the ENM and their effect on fluctuation free energies confirm previously experimentally identified bioactive residues, but also suggest several new candidate regions that are distant from the active site, yet control the protease function. Our results suggest new dynamically driven control regions as possible candidates for non-competitive inhibiting binding sites in the protease, which may assist the development of current fragment-based binding screens. The results also provide new insights into the active biophysical research field of protein fluctuation allostery and its underpinning dynamical structure.
DOI: 10.6084/m9.figshare.13488884
title: 6lu7-croscor-25-0.xlsx from Computational analysis of dynamic allostery and control in the SARS-CoV-2 main protease

description: The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has no publicly-available vaccine or antiviral drugs at the time of writing. An attractive coronavirus drug target is the main protease (M<sup>pro</sup>, also known as 3CL<sup>pro</sup>) because of its vital role in the viral cycle. A significant body of work has been focused on finding inhibitors which bind and block the active site of the main protease, but little has been done to address potential non-competitive inhibition, targeting regions other than the active site, partly because the fundamental biophysics of such allosteric control is still poorly understood. In this work, we construct an Elastic Network Model (ENM) of the SARS-CoV-2 M<sup>pro</sup> homodimer protein and analyse its dynamics and thermodynamics. We found a rich and heterogeneous dynamical structure, including allosterically correlated motions between the homodimeric protease's active sites. Exhaustive 1-point and 2-point mutation scans of the ENM and their effect on fluctuation free energies confirm previously experimentally identified bioactive residues, but also suggest several new candidate regions that are distant from the active site, yet control the protease function. Our results suggest new dynamically driven control regions as possible candidates for non-competitive inhibiting binding sites in the protease, which may assist the development of current fragment-based binding screens. The results also provide new insights into the active biophysical research field of protein fluctuation allostery and its underpinning dynamical structure.
DOI: 10.6084/m9.figshare.13070708
title: Raw_data_population_flowering.xlsx

description: Aphid populations on willow species and hybrids were monitored weekly and its infestation on flowering phenology and catkin production were estimated after inoculating willow trees with 10 adult aphid per plant.
DOI: 10.6084/m9.figshare.13070708.v1
title: Raw_data_population_flowering.xlsx

description: Aphid populations on willow species and hybrids were monitored weekly and its infestation on flowering phenology and catkin production were estimated after inoculating willow trees with 10 adult aphid per plant.
DOI: 10.21227/nw42-j794
title: Holoscopic 3D Micro-Gesture Database

description: HoMG database was recorded using a holoscopic 3D camera, which have 3 conventional gestures from 40 participants under different settings and conditions. The principle of holoscopic 3D (H3D) imaging mimics fly’s eye technique that captures a true 3D optical model of the scene using a microlens array. For the purpose of H3D micro-gesture recognition. HoMG database has two subsets. The video subset has 960 videos and the image subset has 30635 images, while both have three type of microgestures (classes). Each subset has been devided into three partitions: training set, validation set and testing set where there is not overlap between them in term of the subjects. The database has been used for Holoscopic Micro-Gesture Recognition Challenge 2018 (HoMGR 2018) that was held at IEEE Face & Gesture 2018 (FG2018 ) - Xi'an, China, 15-19th May 2018 (https://fg2018.cse.sc.edu/Challenges.html). The database is now public available for wider research community in the research areas of holoscopic 3D image processing, machine learning for gesture recognition and its application in AR and VR.
DOI: 10.6084/m9.figshare.13488894
title: Seasonal abundance of Tuberolachnus salignus and its effect on flowering of host willows of varying susceptibility

description: Aphid populations on willow species and hybrids were monitored weekly and its infestation on flowering phenology and catkin production were estimated after inoculating willow trees with 10 adult aphid per plant.
DOI: 10.6084/m9.figshare.13488894.v1
title: Seasonal abundance of Tuberolachnus salignus and its effect on flowering of host willows of varying susceptibility

description: Aphid populations on willow species and hybrids were monitored weekly and its infestation on flowering phenology and catkin production were estimated after inoculating willow trees with 10 adult aphid per plant.
DOI: 10.6084/m9.figshare.13488847
title: 6lu7-2point-25-K2K1-4.00.xlsx from Computational analysis of dynamic allostery and control in the SARS-CoV-2 main protease

description: The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has no publicly-available vaccine or antiviral drugs at the time of writing. An attractive coronavirus drug target is the main protease (M<sup>pro</sup>, also known as 3CL<sup>pro</sup>) because of its vital role in the viral cycle. A significant body of work has been focused on finding inhibitors which bind and block the active site of the main protease, but little has been done to address potential non-competitive inhibition, targeting regions other than the active site, partly because the fundamental biophysics of such allosteric control is still poorly understood. In this work, we construct an Elastic Network Model (ENM) of the SARS-CoV-2 M<sup>pro</sup> homodimer protein and analyse its dynamics and thermodynamics. We found a rich and heterogeneous dynamical structure, including allosterically correlated motions between the homodimeric protease's active sites. Exhaustive 1-point and 2-point mutation scans of the ENM and their effect on fluctuation free energies confirm previously experimentally identified bioactive residues, but also suggest several new candidate regions that are distant from the active site, yet control the protease function. Our results suggest new dynamically driven control regions as possible candidates for non-competitive inhibiting binding sites in the protease, which may assist the development of current fragment-based binding screens. The results also provide new insights into the active biophysical research field of protein fluctuation allostery and its underpinning dynamical structure.
DOI: 10.6084/m9.figshare.13488844
title: 6lu7-1.pdb from Computational analysis of dynamic allostery and control in the SARS-CoV-2 main protease

description: The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has no publicly-available vaccine or antiviral drugs at the time of writing. An attractive coronavirus drug target is the main protease (M<sup>pro</sup>, also known as 3CL<sup>pro</sup>) because of its vital role in the viral cycle. A significant body of work has been focused on finding inhibitors which bind and block the active site of the main protease, but little has been done to address potential non-competitive inhibition, targeting regions other than the active site, partly because the fundamental biophysics of such allosteric control is still poorly understood. In this work, we construct an Elastic Network Model (ENM) of the SARS-CoV-2 M<sup>pro</sup> homodimer protein and analyse its dynamics and thermodynamics. We found a rich and heterogeneous dynamical structure, including allosterically correlated motions between the homodimeric protease's active sites. Exhaustive 1-point and 2-point mutation scans of the ENM and their effect on fluctuation free energies confirm previously experimentally identified bioactive residues, but also suggest several new candidate regions that are distant from the active site, yet control the protease function. Our results suggest new dynamically driven control regions as possible candidates for non-competitive inhibiting binding sites in the protease, which may assist the development of current fragment-based binding screens. The results also provide new insights into the active biophysical research field of protein fluctuation allostery and its underpinning dynamical structure.
DOI: 10.25646/7778
title: Tagesdaten-CSV aus dem DIVI-Intensivregister

description: Die Tagesdaten-CSV entspricht einem Auszug der Daten des DIVI-Intensivregisters. Die Datei enthält eine Aggregation der aktuellsten Meldungen pro Landkreis. Es werden die aktuell gemeldeten Anzahlen der COVID-19 Intensivfälle sowie die gemeldeten intensivmedizinischen Behandlungskapazitäten angezeigt. Die Tagesdaten-CSV liefert dabei ausschließlich einen Blick auf die Daten gemäß dem Stand des betrachteten Tages. Die Daten sind im situationsbedingten Kontext aufbereitet, damit sind verschiedene Tagesdaten-CSVs u.U. nicht direkt miteinander vergleichbar. Die aktuellsten Meldungen werden im gewählten Betrachtungszeitfenster über alle Meldebereiche und Standorte aufsummiert. Weitere Informationen sind zu finden unter https://www.intensivregister.de/#/faq
DOI: 10.21227/944n-hg64
title: Appendix

description: Appendix for the submitted paper
DOI: 10.21227/rv0s-3t93
title: Holoscopic 3D Micro-Gesture Database

description: HoMG database was recorded using a holoscopic 3D camera, which have 3 conventional gestures from 40 participants under different settings and conditions. The principle of holoscopic 3D (H3D) imaging mimics fly’s eye technique that captures a true 3D optical model of the scene using a microlens array. For the purpose of H3D micro-gesture recognition. HoMG database has two subsets. The video subset has 960 videos and the image subset has 30635 images, while both have three type of microgestures (classes). Each subset has been devided into three partitions: training set, validation set and testing set where there is not overlap between them in term of the subjects. The database has been used for Holoscopic Micro-Gesture Recognition Challenge 2018 (HoMGR 2018) that was held at IEEE Face & Gesture 2018 (FG2018 ) - Xi'an, China, 15-19th May 2018 (https://fg2018.cse.sc.edu/Challenges.html). The database is now public available for wider research community in the research areas of holoscopic 3D image processing, machine learning for gesture recognition and its application in AR and VR.
DOI: 10.21227/ng92-fq44
title: Holoscopic 3D Micro-Gesture Database

description: HoMG database was recorded using a holoscopic 3D camera, which have 3 conventional gestures from 40 participants under different settings and conditions. The principle of holoscopic 3D (H3D) imaging mimics fly’s eye technique that captures a true 3D optical model of the scene using a microlens array. For the purpose of H3D micro-gesture recognition. HoMG database has two subsets. The video subset has 960 videos and the image subset has 30635 images, while both have three type of microgestures (classes). Each subset has been devided into three partitions: training set, validation set and testing set where there is not overlap between them in term of the subjects. The database has been used for Holoscopic Micro-Gesture Recognition Challenge 2018 (HoMGR 2018) that was held at IEEE Face & Gesture 2018 (FG2018 ) - Xi'an, China, 15-19th May 2018 (https://fg2018.cse.sc.edu/Challenges.html). The database is now public available for wider research community in the research areas of holoscopic 3D image processing, machine learning for gesture recognition and its application in AR and VR.
DOI: 10.5519/qd.ztl8rgud
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (531 records)
DOI: 10.21227/g9s1-0347
title: Holoscopic 3D Micro-Gesture Database

description: HoMG database was recorded using a holoscopic 3D camera, which have 3 conventional gestures from 40 participants under different settings and conditions. The principle of holoscopic 3D (H3D) imaging mimics fly’s eye technique that captures a true 3D optical model of the scene using a microlens array. For the purpose of H3D micro-gesture recognition. HoMG database has two subsets. The video subset has 960 videos and the image subset has 30635 images, while both have three type of microgestures (classes). Each subset has been devided into three partitions: training set, validation set and testing set where there is not overlap between them in term of the subjects. The database has been used for Holoscopic Micro-Gesture Recognition Challenge 2018 (HoMGR 2018) that was held at IEEE Face & Gesture 2018 (FG2018 ) - Xi'an, China, 15-19th May 2018 (https://fg2018.cse.sc.edu/Challenges.html). The database is now public available for wider research community in the research areas of holoscopic 3D image processing, machine learning for gesture recognition and its application in AR and VR.
DOI: 10.6084/m9.figshare.12331400
title: Reference carbon cycle dataset for typical Chinese forests via colocated observations and data assimilation

description: Chinese forests cover most of the representative forest types in the Northern Hemisphere and function as a large carbon (C) sink in the global C cycle. The availability of long-term C dynamics observations is key to evaluating and understanding C sequestration of these forests. The Chinese Ecosystem Research Network has conducted normalized and systematic monitoring of the soil-biology-atmosphere-water cycle in Chinese forests since 2000. For the first time, a reference dataset of the decadal C cycle dynamics was produced for 10 typical Chinese forests after strict quality control, including biomass, leaf area index, litterfall, soil organic C, and the corresponding meteorological data. Based on these basic but time-discrete C-cycle elements, an assimilated dataset of key C cycle parameters and time-continuous C sequestration functions was generated via model-data fusion, including C allocation, turnover, and soil, vegetation, and ecosystem C storage. These reference data could be used as a benchmark for model development, evaluation and C cycle research under global climate change for typical forests in the Northern Hemisphere.
DOI: 10.6084/m9.figshare.12331400.v1
title: Reference carbon cycle dataset for typical Chinese forests via colocated observations and data assimilation

description: Chinese forests cover most of the representative forest types in the Northern Hemisphere and function as a large carbon (C) sink in the global C cycle. The availability of long-term C dynamics observations is key to evaluating and understanding C sequestration of these forests. The Chinese Ecosystem Research Network has conducted normalized and systematic monitoring of the soil-biology-atmosphere-water cycle in Chinese forests since 2000. For the first time, a reference dataset of the decadal C cycle dynamics was produced for 10 typical Chinese forests after strict quality control, including biomass, leaf area index, litterfall, soil organic C, and the corresponding meteorological data. Based on these basic but time-discrete C-cycle elements, an assimilated dataset of key C cycle parameters and time-continuous C sequestration functions was generated via model-data fusion, including C allocation, turnover, and soil, vegetation, and ecosystem C storage. These reference data could be used as a benchmark for model development, evaluation and C cycle research under global climate change for typical forests in the Northern Hemisphere.
DOI: 10.5517/ccdc.csd.cc259mz3
title: CCDC 2005265: Experimental Crystal Structure Determination

description: Related Article: Alexander Kroll, Henning Steinert, Mike Jörges, Tim Steinke, Bert Mallick, Viktoria H. Gessner|2020|Organometallics|39|4312|doi:10.1021/acs.organomet.0c00412
DOI: 10.5517/ccdc.csd.cc259n05
title: CCDC 2005266: Experimental Crystal Structure Determination

description: Related Article: Alexander Kroll, Henning Steinert, Mike Jörges, Tim Steinke, Bert Mallick, Viktoria H. Gessner|2020|Organometallics|39|4312|doi:10.1021/acs.organomet.0c00412
DOI: 10.5517/ccdc.csd.cc259n16
title: CCDC 2005267: Experimental Crystal Structure Determination

description: Related Article: Alexander Kroll, Henning Steinert, Mike Jörges, Tim Steinke, Bert Mallick, Viktoria H. Gessner|2020|Organometallics|39|4312|doi:10.1021/acs.organomet.0c00412
DOI: 10.5517/ccdc.csd.cc259n27
title: CCDC 2005268: Experimental Crystal Structure Determination

description: Related Article: Alexander Kroll, Henning Steinert, Mike Jörges, Tim Steinke, Bert Mallick, Viktoria H. Gessner|2020|Organometallics|39|4312|doi:10.1021/acs.organomet.0c00412
DOI: 10.5517/ccdc.csd.cc259n38
title: CCDC 2005269: Experimental Crystal Structure Determination

description: Related Article: Alexander Kroll, Henning Steinert, Mike Jörges, Tim Steinke, Bert Mallick, Viktoria H. Gessner|2020|Organometallics|39|4312|doi:10.1021/acs.organomet.0c00412
DOI: 10.5517/ccdc.csd.cc259n49
title: CCDC 2005270: Experimental Crystal Structure Determination

description: Related Article: Alexander Kroll, Henning Steinert, Mike Jörges, Tim Steinke, Bert Mallick, Viktoria H. Gessner|2020|Organometallics|39|4312|doi:10.1021/acs.organomet.0c00412
DOI: 10.5517/ccdc.csd.cc259n5b
title: CCDC 2005271: Experimental Crystal Structure Determination

description: Related Article: Alexander Kroll, Henning Steinert, Mike Jörges, Tim Steinke, Bert Mallick, Viktoria H. Gessner|2020|Organometallics|39|4312|doi:10.1021/acs.organomet.0c00412