cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/vsyfmw
title: Saxifraga damingshanensis (S. sect. Irregulares, Saxifragaceae), a new species from Guangxi, China

description: This dataset contains the digitized treatments in Plazi based on the original journal article Zhao, Wan-Yi, Meng, Kai-Kai, Fan, Qiang, Jin, Jian-Hua, Liao, Wen-Bo (2019): Saxifraga damingshanensis (S. sect. Irregulares, Saxifragaceae), a new species from Guangxi, China. PhytoKeys 133: 95-103, DOI: http://dx.doi.org/10.3897/phytokeys.133.36704, URL: http://dx.doi.org/10.3897/phytokeys.133.36704
DOI: 10.15468/bxwxl4
title: Diaporthalean fungi associated with canker and dieback of trees from Mount Dongling in Beijing, China

description: This dataset contains the digitized treatments in Plazi based on the original journal article Zhu, Haiyan, Pan, Meng, Bonthond, Guido, Tian, Chengming, Fan, Xinlei (2019): Diaporthalean fungi associated with canker and dieback of trees from Mount Dongling in Beijing, China. MycoKeys 59: 67-94, DOI: http://dx.doi.org/10.3897/mycokeys.59.38055, URL: http://dx.doi.org/10.3897/mycokeys.59.38055
DOI: 10.25919/5da80996af3fa
title: CCS - MV Bluefin 2018 V02 Multibeam Echosounder

description: roject Overview: A range of solutions will be required to reach globally agreed emissions reductions targets for carbon dioxide (CO2). Carbon capture and storage (CCS) is part of the suite of technologies that will contribute to lowering atmospheric emissions of CO2 from Australia's energy system. There are a wide variety of technologies at various stages of technical and commercial readiness, with more development underway for cost effective CO2 capture and storage. Our research will provide new knowledge to inform cost-efficient measurement, monitoring and verification (MMV) of the environment of CCS projects in coastal waters. --o-- Kongsberg EM2040c Multibeam Echosounder – This multibeam echosounder is a bathymetric echosounder that has a frequency range of 200kHz- 400kHz. Two transducers were used mounted at 30° to increase across track coverage, commonly known as a dual head setup. The data was collected in dual swath mode to increase the alongtrack resolution. Oceans and Atmosphere. Relevant component details: make, model, serial number, firmware version, settings: Kongsberg EM2040C Head 1, S/N: 113, 300kHz;Continuouse Wave; High Density Equidistant;Dual Head; Dual Swath Kongsberg EM2040C Head 2, S/N 1403, 300kHz;Continuouse Wave; High Density Equidistant;Dual Head; Dual Swath 2 x Processing Units, S/N’s 100011 and 20087, Processing unit 100011 was on loan from Geoscience Australia PosMV Positioning and Navigation System, S/N 8438 Valeport Monitor SVP 500, S/N38500, Set to self-record profile Valeport MiniSVS Calibration Information: Calibration of the multibeam echosounder was conducted prior to survey on the transit to site. A second set of calibration lines were run on site for confirmation. Results were applied in post processing. Name(s) and acquisition software used: Multibeam bathymetry, Multibeam backscatter, Multibeam water column acquired using SIS (Seafloor Information System)
DOI: 10.15468/bs0kht
title: European species of Dendrostoma (Diaporthales)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Jaklitsch, Walter M., Voglmayr, Hermann (2019): European species of Dendrostoma (Diaporthales). MycoKeys 59: 1-26, DOI: http://dx.doi.org/10.3897/mycokeys.59.37966, URL: http://dx.doi.org/10.3897/mycokeys.59.37966
DOI: 10.25345/c5867q
title: MassIVE MSV000084465 - GNPS-HONGYACHI-300-2000-POSITIVE
title: With the continued growth in shallow-intermediate reservoirs exploration, the difficulty of oil and gas discovery is increasing, and the exploration for deep petroleum accumulations has become an important area around the world. The new reserves of deep oil and gas around the world show a significant growth trend. However, the generation, evolution and preservation of deep oil and gas are the hot and difficult points in petroleum geochemistry.
DOI: 10.17632/f5r84kdkzf.1
title: Cows for Future

description: In the framework of an interdisciplinary reseach seminar (Q-Team) students from Humboldt University of Berlin got to know and tried out data analyitical tools to investigate microclimate in open livestock buildings and implications on environment (pollutant emission) and animal welfare (climate induced stress) . Within the first seminar sessions each of the students selected an aspect of the topic and developed a research design. Within the seminar the individual research questions were jointly investigated and discussed. The manuscript „cows for future“ complies the results of this research based learning in one comprehensive paper.
DOI: 10.21227/3fp9-n664
title: Occupant-Induced Office Floor Vibration Dataset

description: We have collected vibration data caused by occupant activity in a campus building in Shenzhen, China.This dataset is utilizing structural vibrationsto detect occupant information by capturing the occupant-inducedvibration signals on the floor.
DOI: 10.17632/9rwzkjs9mw.1
title: The ER-localized transmembrane protein TMEM39A/SUSR2 regulates autophagy by controlling the trafficking of the PtdIns(4)P phosphatase SAC1. Miao et al.

description: All raw data for MOLECULAR-CELL-19-01673
DOI: 10.25345/c54h32
title: MassIVE MSV000084466 - GNPS-HONGYUAN-20-40CM-300-2000-POSITIVE
title: With the continued growth in shallow-intermediate reservoirs exploration, the difficulty of oil and gas discovery is increasing, and the exploration for deep petroleum accumulations has become an important area around the world. The new reserves of deep oil and gas around the world show a significant growth trend. However, the generation, evolution and preservation of deep oil and gas are the hot and difficult points in petroleum geochemistry.
DOI: 10.5281/zenodo.3465883
title: Homology modelling, molecular docking and molecular dynamics simulations of wild type and mutant human CYP2J2 with three polyunsaturated fatty acids

description: This is the "parent" repository for the Data Note : "­Molecular dynamics simulations of the interaction of wild type and mutant human CYP2J2 with polyunsaturated fatty acids" by Abelak, Bishop-Bailey and Nobeli. It contains a document (<strong>Abelak_etal_Methods.pdf</strong>) describing the methods used to produce the data here and the data in all repositories supplementing it. It also contains a shell script (<strong>create_sim4_repeats.sh</strong>) that is typical of those used to set up the molecular dynamics simulations in the repositories supplementing this one. Finally, it contains the results of the homology modelling and docking simulations that formed the starting points for the molecular dynamics simulations in this study. Description of files in this dataset: <strong>C2J2_min3_mod_noH.pdb</strong> : Homology model of the wild type CYP2J2 built from an alignment of templates with PDB ids: 1SUO, 2P85, 3EBS and 1Z10. <strong>docking_wild_type_C2J2.zip</strong> : Nine docked poses of arachidonic acid docked to the homology model of the wild type CYP2J2. Details of how this data was produced is available in the Abelak_etal_Methods.docx document.
description: Funding and acknowledgments KKA was supported by a PhD studentship from the London Interdisciplinary Biosciences Consortium (LIDo) BBSRC Doctoral Training Partnership programme. The work presented here made use of Emerald, a GPU-accelerated High Performance Computer, made available by the Science and Engineering South Consortium operated in partnership with the STFC Rutherford-Appleton Laboratory.
DOI: 10.5281/zenodo.3465884
title: Homology modelling, molecular docking and molecular dynamics simulations of wild type and mutant human CYP2J2 with three polyunsaturated fatty acids

description: This is the "parent" repository for the Data Note : "­Molecular dynamics simulations of the interaction of wild type and mutant human CYP2J2 with polyunsaturated fatty acids" by Abelak, Bishop-Bailey and Nobeli. It contains a document (<strong>Abelak_etal_Methods.pdf</strong>) describing the methods used to produce the data here and the data in all repositories supplementing it. It also contains a shell script (<strong>create_sim4_repeats.sh</strong>) that is typical of those used to set up the molecular dynamics simulations in the repositories supplementing this one. Finally, it contains the results of the homology modelling and docking simulations that formed the starting points for the molecular dynamics simulations in this study. Description of files in this dataset: <strong>C2J2_min3_mod_noH.pdb</strong> : Homology model of the wild type CYP2J2 built from an alignment of templates with PDB ids: 1SUO, 2P85, 3EBS and 1Z10. <strong>docking_wild_type_C2J2.zip</strong> : Nine docked poses of arachidonic acid docked to the homology model of the wild type CYP2J2. Details of how this data was produced is available in the Abelak_etal_Methods.docx document.
description: Funding and acknowledgments KKA was supported by a PhD studentship from the London Interdisciplinary Biosciences Consortium (LIDo) BBSRC Doctoral Training Partnership programme. The work presented here made use of Emerald, a GPU-accelerated High Performance Computer, made available by the Science and Engineering South Consortium operated in partnership with the STFC Rutherford-Appleton Laboratory.
DOI: 10.21227/pczt-1s21
title: Occupant-Induced Office Floor Vibration Dataset

description: We have collected vibration data caused by occupant activity in a campus building in Shenzhen, China.This dataset is utilizing structural vibrationsto detect occupant information by capturing the occupant-inducedvibration signals on the floor.
DOI: 10.5281/zenodo.3465589
title: Molecular dynamics simulations of the interaction of wild type human CYP2J2 with arachidonic acid (POSES 1 and 2)

description: <strong>Description of files in this dataset:</strong> <strong>MD_wt_CYP2J2_AA_StateX_repeatY.zip</strong> : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of wild type CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 4 times, hence there are 4 repeats per pose). Each directory contains the following sub-directories: 001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands 002.min : Minimisation stage 003.heat : Heating stage 004.equil: Equilibration stage 005.md : Production stage 006.analysis : Basic energy graphs 007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)
description: See Abelak_etal_Methods.pdf in 10.5281/zenodo.3465884 for details of how the data were produced. Funding and acknowledgments KKA was supported by a PhD studentship from the London Interdisciplinary Biosciences Consortium (LIDo) BBSRC Doctoral Training Partnership programme. The work presented here made use of Emerald, a GPU-accelerated High Performance Computer, made available by the Science and Engineering South Consortium operated in partnership with the STFC Rutherford-Appleton Laboratory.
DOI: 10.5281/zenodo.3465590
title: Molecular dynamics simulations of the interaction of wild type human CYP2J2 with arachidonic acid (POSES 1 and 2)

description: <strong>Description of files in this dataset:</strong> <strong>MD_wt_CYP2J2_AA_StateX_repeatY.zip</strong> : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of wild type CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 4 times, hence there are 4 repeats per pose). Each directory contains the following sub-directories: 001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands 002.min : Minimisation stage 003.heat : Heating stage 004.equil: Equilibration stage 005.md : Production stage 006.analysis : Basic energy graphs 007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)
description: See Abelak_etal_Methods.pdf in 10.5281/zenodo.3465884 for details of how the data were produced. Funding and acknowledgments KKA was supported by a PhD studentship from the London Interdisciplinary Biosciences Consortium (LIDo) BBSRC Doctoral Training Partnership programme. The work presented here made use of Emerald, a GPU-accelerated High Performance Computer, made available by the Science and Engineering South Consortium operated in partnership with the STFC Rutherford-Appleton Laboratory.
DOI: 10.5281/zenodo.3466691
title: Molecular dynamics simulations of the interaction of wild type human CYP2J2 with arachidonic acid (POSES 3 and 4)

description: <strong>Description of files in this dataset:</strong> <strong>MD_wt_CYP2J2_AA_StateX_repeatY.zip</strong> : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of wild type CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 4 times, hence there are 4 repeats per pose). Each directory contains the following sub-directories: 001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands 002.min : Minimisation stage 003.heat : Heating stage 004.equil: Equilibration stage 005.md : Production stage 006.analysis : Basic energy graphs 007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)
description: See Abelak_etal_Methods.pdf in 10.5281/zenodo.3465884 for details of how the data were produced. Funding and acknowledgments KKA was supported by a PhD studentship from the London Interdisciplinary Biosciences Consortium (LIDo) BBSRC Doctoral Training Partnership programme. The work presented here made use of Emerald, a GPU-accelerated High Performance Computer, made available by the Science and Engineering South Consortium operated in partnership with the STFC Rutherford-Appleton Laboratory.
DOI: 10.5281/zenodo.3466692
title: Molecular dynamics simulations of the interaction of wild type human CYP2J2 with arachidonic acid (POSES 3 and 4)

description: <strong>Description of files in this dataset:</strong> <strong>MD_wt_CYP2J2_AA_StateX_repeatY.zip</strong> : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of wild type CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 4 times, hence there are 4 repeats per pose). Each directory contains the following sub-directories: 001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands 002.min : Minimisation stage 003.heat : Heating stage 004.equil: Equilibration stage 005.md : Production stage 006.analysis : Basic energy graphs 007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)
description: See Abelak_etal_Methods.pdf in 10.5281/zenodo.3465884 for details of how the data were produced. Funding and acknowledgments KKA was supported by a PhD studentship from the London Interdisciplinary Biosciences Consortium (LIDo) BBSRC Doctoral Training Partnership programme. The work presented here made use of Emerald, a GPU-accelerated High Performance Computer, made available by the Science and Engineering South Consortium operated in partnership with the STFC Rutherford-Appleton Laboratory.
DOI: 10.5281/zenodo.3473885
title: Molecular dynamics simulations of the interaction of wild type human CYP2J2 with arachidonic acid (POSES 5 and 6)

description: <strong>Description of files in this dataset:</strong> <strong>MD_wt_CYP2J2_AA_StateX_repeatY.zip</strong> : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of wild type CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 4 times, hence there are 4 repeats per pose). Each directory contains the following sub-directories: 001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands 002.min : Minimisation stage 003.heat : Heating stage 004.equil: Equilibration stage 005.md : Production stage 006.analysis : Basic energy graphs 007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)
description: See Abelak_etal_Methods.pdf in 10.5281/zenodo.3465884 for details of how the data were produced. Funding and acknowledgments KKA was supported by a PhD studentship from the London Interdisciplinary Biosciences Consortium (LIDo) BBSRC Doctoral Training Partnership programme. The work presented here made use of Emerald, a GPU-accelerated High Performance Computer, made available by the Science and Engineering South Consortium operated in partnership with the STFC Rutherford-Appleton Laboratory.
DOI: 10.5281/zenodo.3473886
title: Molecular dynamics simulations of the interaction of wild type human CYP2J2 with arachidonic acid (POSES 5 and 6)

description: <strong>Description of files in this dataset:</strong> <strong>MD_wt_CYP2J2_AA_StateX_repeatY.zip</strong> : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of wild type CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 4 times, hence there are 4 repeats per pose). Each directory contains the following sub-directories: 001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands 002.min : Minimisation stage 003.heat : Heating stage 004.equil: Equilibration stage 005.md : Production stage 006.analysis : Basic energy graphs 007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)
description: See Abelak_etal_Methods.pdf in 10.5281/zenodo.3465884 for details of how the data were produced. Funding and acknowledgments KKA was supported by a PhD studentship from the London Interdisciplinary Biosciences Consortium (LIDo) BBSRC Doctoral Training Partnership programme. The work presented here made use of Emerald, a GPU-accelerated High Performance Computer, made available by the Science and Engineering South Consortium operated in partnership with the STFC Rutherford-Appleton Laboratory.
DOI: 10.5281/zenodo.3473908
title: Molecular dynamics simulations of the interaction of wild type human CYP2J2 with DHA (POSES 1-4)

description: <strong>Description of files in this dataset:</strong> <strong>MD_wt_CYP2J2_DHA_StateX_repeatY.zip</strong> : Series of zipped directories for molecular dynamics simulations of docosahexaenoic acid (DHA) in the active site of wild type CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 4 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 3 times, hence there are 3 repeats per pose). Each directory contains the following sub-directories: 001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands 002.min : Minimisation stage 003.heat : Heating stage 004.equil: Equilibration stage 005.md : Production stage 006.analysis : Basic energy graphs 007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)
description: See Abelak_etal_Methods.pdf in 10.5281/zenodo.3465884 for details of how the data were produced. Funding and acknowledgments KKA was supported by a PhD studentship from the London Interdisciplinary Biosciences Consortium (LIDo) BBSRC Doctoral Training Partnership programme. The work presented here made use of Emerald, a GPU-accelerated High Performance Computer, made available by the Science and Engineering South Consortium operated in partnership with the STFC Rutherford-Appleton Laboratory.
DOI: 10.5281/zenodo.3473909
title: Molecular dynamics simulations of the interaction of wild type human CYP2J2 with DHA (POSES 1-4)

description: <strong>Description of files in this dataset:</strong> <strong>MD_wt_CYP2J2_DHA_StateX_repeatY.zip</strong> : Series of zipped directories for molecular dynamics simulations of docosahexaenoic acid (DHA) in the active site of wild type CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 4 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 3 times, hence there are 3 repeats per pose). Each directory contains the following sub-directories: 001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands 002.min : Minimisation stage 003.heat : Heating stage 004.equil: Equilibration stage 005.md : Production stage 006.analysis : Basic energy graphs 007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)
description: See Abelak_etal_Methods.pdf in 10.5281/zenodo.3465884 for details of how the data were produced. Funding and acknowledgments KKA was supported by a PhD studentship from the London Interdisciplinary Biosciences Consortium (LIDo) BBSRC Doctoral Training Partnership programme. The work presented here made use of Emerald, a GPU-accelerated High Performance Computer, made available by the Science and Engineering South Consortium operated in partnership with the STFC Rutherford-Appleton Laboratory.
DOI: 10.5519/qd.vlxg0cql
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (49 records)
DOI: 10.5281/zenodo.3473926
title: Molecular dynamics simulations of the interaction of wild type human CYP2J2 with EPA (POSES 1-4)

description: <strong>Description of files in this dataset:</strong> <strong>MD_wt_CYP2J2_EPA_StateX_repeatY.zip</strong> : Series of zipped directories for molecular dynamics simulations of eicosapentaenoic acid (EPA) in the active site of wild type CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 4 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 3 times, hence there are 3 repeats per pose). Each directory contains the following sub-directories: 001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands 002.min : Minimisation stage 003.heat : Heating stage 004.equil: Equilibration stage 005.md : Production stage 006.analysis : Basic energy graphs 007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)
description: See Abelak_etal_Methods.pdf in 10.5281/zenodo.3465884 for details of how the data were produced. Funding and acknowledgments KKA was supported by a PhD studentship from the London Interdisciplinary Biosciences Consortium (LIDo) BBSRC Doctoral Training Partnership programme. The work presented here made use of Emerald, a GPU-accelerated High Performance Computer, made available by the Science and Engineering South Consortium operated in partnership with the STFC Rutherford-Appleton Laboratory.