cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14063338
title: Molecular Dynamics Trajectories for GPR6 Basal Activity (Volume 03)

description: Molecular Dynamics Data for 10.1126/scisignal.ado8741 for publication at Science Signalling

Barekatain M., Johansson L.C., Lam J.H. et al Structural Insights into the High Basal Activity and Inverse Agonism of the Orphan Receptor GPR6 Implicated in Parkinson's Disease, Sci Signal. 2024 Dec 3;17(865):eado8741. doi: 10.1126/scisignal.ado8741. Epub 2024 Dec 3.

Instruction

The compressed folder contains the PDB format file ("Topology") and the XTC format file (Trajectories). The timestep in this strided trajectory is 0.1 ns per frame.The compression was created with, for example,

`tar czpvf - ./Nolig_Respawn00/ | split -d -b 5000M - Nolig_Respawn00a.tar.`

They can be decompressed with 

`cat Nolig_Respawn00a.tar.* | tar xzpvf -`

 

Remarks



Trajectories in Respawn00 are only used as an initial sampling round. Trajectories in Respawn01 are the final sampling round for building Markov state model.

There are in total 4 Volumes of Respawn01 data. Currently, the union of these volumes must be downloaded before decompression. See https://zenodo.org/communities/mdtrajectorygpr6/records?q=&l=list&p=1&s=10&sort=newest

For trajectories without keyword 'fitted', the Periodic boundary condition (PBC) can be restored using VMD's standard pbc commands. For`*fitted*.xtc`, the protein has already been centered and the PBC is destroyed for the sake of visual inspection only. 


 

Please cite us if you find this data useful!
DOI: 10.5281/zenodo.14061359
title: Molecular Dynamics Trajectories for GPR6 Basal Activity (Volume 01)

description: Molecular Dynamics Data for 10.1126/scisignal.ado8741 for publication at Science Signalling

Barekatain M., Johansson L.C., Lam J.H. et al Structural Insights into the High Basal Activity and Inverse Agonism of the Orphan Receptor GPR6 Implicated in Parkinson's Disease, Sci Signal. 2024 Dec 3;17(865):eado8741. doi: 10.1126/scisignal.ado8741. Epub 2024 Dec 3.

Instruction

The compressed folder contains the PDB format file ("Topology") and the XTC format file (Trajectories). The timestep in this strided trajectory is 0.1 ns per frame.The compression was created with, for example,

`tar czpvf - ./Nolig_Respawn00/ | split -d -b 5000M - Nolig_Respawn00a.tar.`

They can be decompressed with 

`cat Nolig_Respawn00a.tar.* | tar xzpvf -`

 

Remarks



Trajectories in Respawn00 are only used as an initial sampling round. Trajectories in Respawn01 are the final sampling round for building Markov state model.

There are in total 4 Volumes of Respawn01 data. Currently, the union of these volumes must be downloaded before decompression. See https://zenodo.org/communities/mdtrajectorygpr6/records?q=&l=list&p=1&s=10&sort=newest

For trajectories without keyword 'fitted', the Periodic boundary condition (PBC) can be restored using VMD's standard pbc commands. For`*fitted*.xtc`, the protein has already been centered and the PBC is destroyed for the sake of visual inspection only. 


Please cite us if you find this data useful!
DOI: 10.5281/zenodo.14061360
title: Molecular Dynamics Trajectories for GPR6 Basal Activity (Volume 01)

description: Molecular Dynamics Data for 10.1126/scisignal.ado8741 for publication at Science Signalling

Barekatain M., Johansson L.C., Lam J.H. et al Structural Insights into the High Basal Activity and Inverse Agonism of the Orphan Receptor GPR6 Implicated in Parkinson's Disease, Sci Signal. 2024 Dec 3;17(865):eado8741. doi: 10.1126/scisignal.ado8741. Epub 2024 Dec 3.

Instruction

The compressed folder contains the PDB format file ("Topology") and the XTC format file (Trajectories). The timestep in this strided trajectory is 0.1 ns per frame.The compression was created with, for example,

`tar czpvf - ./Nolig_Respawn00/ | split -d -b 5000M - Nolig_Respawn00a.tar.`

They can be decompressed with 

`cat Nolig_Respawn00a.tar.* | tar xzpvf -`

 

Remarks



Trajectories in Respawn00 are only used as an initial sampling round. Trajectories in Respawn01 are the final sampling round for building Markov state model.

There are in total 4 Volumes of Respawn01 data. Currently, the union of these volumes must be downloaded before decompression. See https://zenodo.org/communities/mdtrajectorygpr6/records?q=&l=list&p=1&s=10&sort=newest

For trajectories without keyword 'fitted', the Periodic boundary condition (PBC) can be restored using VMD's standard pbc commands. For`*fitted*.xtc`, the protein has already been centered and the PBC is destroyed for the sake of visual inspection only. 


Please cite us if you find this data useful!
DOI: 10.6084/m9.figshare.28561118
title: DNA methylation profiling

description: DNA methylaiton profiling of cervical cancer samples
DOI: 10.5281/zenodo.14060751
title: Molecular Dynamics Trajectories for GPR6 without Ligand (ApoNoLig)

description: Molecular Dynamics Data for 10.1126/scisignal.ado8741 for publication at Science Signalling

Barekatain M., Johansson L.C., Lam J.H. et al Structural Insights into the High Basal Activity and Inverse Agonism of the Orphan Receptor GPR6 Implicated in Parkinson's Disease, Sci Signal. 2024 Dec 3;17(865):eado8741. doi: 10.1126/scisignal.ado8741. Epub 2024 Dec 3.

This folder contains the PDB format file ("Topology") and the XTC format file (Trajectories). The timestep in this strided trajectory is 0.1 ns per frame. Periodic boundary condition (pbc) can be restored using VMD's standard pbc commands.

Please cite us if you find this data useful!
DOI: 10.5281/zenodo.14060752
title: Molecular Dynamics Trajectories for GPR6 without Ligand (ApoNoLig)

description: Molecular Dynamics Data for 10.1126/scisignal.ado8741 for publication at Science Signalling

Barekatain M., Johansson L.C., Lam J.H. et al Structural Insights into the High Basal Activity and Inverse Agonism of the Orphan Receptor GPR6 Implicated in Parkinson's Disease, Sci Signal. 2024 Dec 3;17(865):eado8741. doi: 10.1126/scisignal.ado8741. Epub 2024 Dec 3.

This folder contains the PDB format file ("Topology") and the XTC format file (Trajectories). The timestep in this strided trajectory is 0.1 ns per frame. Periodic boundary condition (pbc) can be restored using VMD's standard pbc commands.

Please cite us if you find this data useful!
DOI: 10.15468/dl.rwyb63
title: Occurrence Download

description: A dataset containing 25550 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sceloporus grammicus Wiegmann, 1828"
 ]
}

 The dataset includes 25550 records from 106 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009599-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14060679
title: Molecular Dynamics Trajectories for GPR6 with Ligand S1P

description: Molecular Dynamics Data for 10.1126/scisignal.ado8741 for publication at Science Signalling

Barekatain M., Johansson L.C., Lam J.H. et al Structural Insights into the High Basal Activity and Inverse Agonism of the Orphan Receptor GPR6 Implicated in Parkinson's Disease, Sci Signal. 2024 Dec 3;17(865):eado8741. doi: 10.1126/scisignal.ado8741. Epub 2024 Dec 3.

This folder contains the PDB format file ("Topology") and the XTC format file (Trajectories). The timestep in this strided trajectory is 0.1 ns per frame. Periodic boundary condition (pbc) can be restored using VMD's standard pbc commands.

Please cite us if you find this data useful!
DOI: 10.5281/zenodo.14060678
title: Molecular Dynamics Trajectories for GPR6 with Ligand S1P

description: Molecular Dynamics Data for 10.1126/scisignal.ado8741 for publication at Science Signalling

Barekatain M., Johansson L.C., Lam J.H. et al Structural Insights into the High Basal Activity and Inverse Agonism of the Orphan Receptor GPR6 Implicated in Parkinson's Disease, Sci Signal. 2024 Dec 3;17(865):eado8741. doi: 10.1126/scisignal.ado8741. Epub 2024 Dec 3.

This folder contains the PDB format file ("Topology") and the XTC format file (Trajectories). The timestep in this strided trajectory is 0.1 ns per frame. Periodic boundary condition (pbc) can be restored using VMD's standard pbc commands.

Please cite us if you find this data useful!
DOI: 10.15468/dl.9farfw
title: Occurrence Download

description: A dataset containing 1293 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Phoracantha recurva Newman, 1840",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1293 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009694-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vxr8m2
title: Occurrence Download

description: A dataset containing 168 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is one of (North America, South America)",
 "Country is one of (Mexico, United States of America)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "VerbatimScientificName is Centruroides"
 ]
}

 The dataset includes 168 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009696-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.85w7bq
title: Occurrence Download

description: A dataset containing 1510 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Cathartes aura aura"
 ]
}

 The dataset includes 1510 records from 48 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009697-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/10974846
title: WallStreetBets 2022
DOI: 10.6084/m9.figshare.28561151
title: meta data

description: meta data
DOI: 10.6084/m9.figshare.28561151.v2
title: meta data

description: meta data
DOI: 10.6084/m9.figshare.28561151.v1
title: meta data

description: meta data
DOI: 10.6084/m9.figshare.28561148
title: DNA methylation profiling of cervical cancer

description: DNA methylation profiling of cervical cancer
DOI: 10.15468/dl.n44hxe
title: Occurrence Download

description: A dataset containing 883 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Phyllocnistis citrella Stainton, 1856",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 883 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009600-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.znp79y
title: Occurrence Download

description: A dataset containing 238 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Cathartes aura jota (Molina, 1782)"
 ]
}

 The dataset includes 238 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009698-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.28557182
title: ParalellCorpusMixtec-Spanish

description: The publication of this data aims to contribute to the rescue and preservation of the indigenous Mixtec language through the collection of corpora and the development of technologies in the Mixtec language.This data contains 14,587 pairs of Spanish-Mixtec sentences. The data are from 4 categories: Laws, Education, Religion, and Health. In collecting this data, a search was carried out in person and digitally to collect parallel corpora. After the search, the physical texts were scanned. We then conducted a valuable manual data correction and preprocessing process to clean and prepare the data.The majority of the texts collected are from religious and educational categories. This data is valuable in the development of language technologies in the Mixtec language. Our data can be used to develop voice translation models, morpho-syntactic analysis, and spell checkers in the Mixtec language. Our data has valuable contributions since it does not contain duplicate fragments or incomplete or empty sentences. Researchers using our data do not need to scan physical documents, and we correct errors identified in the data.
DOI: 10.15468/dl.n3uq4s
title: Occurrence Download

description: A dataset containing 5468 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Agriotes lineatus (Linnaeus, 1767)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 5468 records from 292 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009700-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wuarv4
title: Occurrence Download

description: A dataset containing 64626 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Agelastica alni (Linnaeus, 1758)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 64626 records from 400 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009691-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f76zpd
title: Occurrence Download

description: A dataset containing 3677 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Larix gmelinii (Rupr.) Kuzen.",
 "HasCoordinate is true",
 "Year is 2000,2023",
 {
 "not" : {
 "BasisOfRecord" : [
 "is Fossil"
 ]
 }
 }
 ]
}

 The dataset includes 3677 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009602-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vzbtx4
title: Occurrence Download

description: A dataset containing 43661 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "Country is Mexico",
 "StateProvince is Jalisco",
 "TaxonKey is Coleoptera"
 ]
}

 The dataset includes 43661 records from 115 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009603-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jj65yg
title: Occurrence Download

description: A dataset containing 954255 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Ranunculus acris L.)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 954255 records from 2945 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009695-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/ccdc.csd.cc1m5fx4
title: CCDC 1494786: Experimental Crystal Structure Determination

description: Related Article: Daniel Upmann, Peter G. Jones|2018|Dalton Trans.|47|2748|doi:10.1039/C7DT04531J
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.cc1m5fy5
title: CCDC 1494787: Experimental Crystal Structure Determination

description: Related Article: Daniel Upmann, Peter G. Jones|2018|Dalton Trans.|47|2748|doi:10.1039/C7DT04531J
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.cc1m5fz6
title: CCDC 1494788: Experimental Crystal Structure Determination

description: Related Article: Daniel Upmann, Peter G. Jones|2018|Dalton Trans.|47|2748|doi:10.1039/C7DT04531J
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.ccxmyv9
title: CCDC 853332: Experimental Crystal Structure Determination

description: Related Article: Milica Milenković, Igor N. Shcherbakov, Leonid D. Popov, Sergey I. Levchenkov, Sergey A. Borodkin, Grigory G. Alexandrov|2017|Polyhedron|121|278|doi:10.1016/j.poly.2016.10.020
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.cc1m5g08
title: CCDC 1494789: Experimental Crystal Structure Determination

description: Related Article: Rob De Vreese, Lisa Galle, Yves Depetter, Jorick Franceus, Tom Desmet, Kristof Van Hecke, Veronick Benoy, Ludo Van Den Bosch, Matthias D'hooghe|2017|Chem.-Eur.J.|23|128|doi:10.1002/chem.201604167
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.ccxmyt8
title: CCDC 853331: Experimental Crystal Structure Determination

description: Related Article: Milica Milenković, Igor N. Shcherbakov, Leonid D. Popov, Sergey I. Levchenkov, Sergey A. Borodkin, Grigory G. Alexandrov|2017|Polyhedron|121|278|doi:10.1016/j.poly.2016.10.020
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.cc1m5g2b
title: CCDC 1494791: Experimental Crystal Structure Determination

description: Related Article: Hana Elshaflu, Tamara R. Todorović, Milan Nikolić, Aleksandar Lolić, Aleksandar Višnjevac, Stefanie Hagenow, José M. Padrón, Alfonso T. García-Sosa, Ivana S. Djordjević, Sonja Grubišić, Holger Stark, Nenad R. Filipović|2018|Frontiers in Chemistry|6|247|doi:10.3389/fchem.2018.00247
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.cc1m5g3c
title: CCDC 1494792: Experimental Crystal Structure Determination

description: Related Article: Hana Elshaflu, Tamara R. Todorović, Milan Nikolić, Aleksandar Lolić, Aleksandar Višnjevac, Stefanie Hagenow, José M. Padrón, Alfonso T. García-Sosa, Ivana S. Djordjević, Sonja Grubišić, Holger Stark, Nenad R. Filipović|2018|Frontiers in Chemistry|6|247|doi:10.3389/fchem.2018.00247
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.cc1m5g4d
title: CCDC 1494793: Experimental Crystal Structure Determination

description: Related Article: Riccardo Suter, Zoltán Benkő, Mark Bispinghoff, Hansjörg Grützmacher|2017|Angew.Chem.,Int.Ed.|56|11226|doi:10.1002/anie.201705473
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.cc1m5g5f
title: CCDC 1494794: Experimental Crystal Structure Determination

description: Related Article: Riccardo Suter, Zoltán Benkő, Mark Bispinghoff, Hansjörg Grützmacher|2017|Angew.Chem.,Int.Ed.|56|11226|doi:10.1002/anie.201705473
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.cc1m5g6g
title: CCDC 1494795: Experimental Crystal Structure Determination

description: Related Article: Riccardo Suter, Zoltán Benkő, Mark Bispinghoff, Hansjörg Grützmacher|2017|Angew.Chem.,Int.Ed.|56|11226|doi:10.1002/anie.201705473
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.cc1m5g7h
title: CCDC 1494796: Experimental Crystal Structure Determination

description: Related Article: Riccardo Suter, Zoltán Benkő, Mark Bispinghoff, Hansjörg Grützmacher|2017|Angew.Chem.,Int.Ed.|56|11226|doi:10.1002/anie.201705473
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.