cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.bcn2ah
title: Occurrence Download

description: A dataset containing 22 species occurrences available in GBIF matching the query:
{
 "SpeciesKey" : [
 "is Lactarius flavidulus S.Imai"
 ]
}

 The dataset includes 22 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0147282-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.675jmz
title: Occurrence Download

description: A dataset containing 243 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Blepharis subvolubilis C.B.Clarke"
 ]
}

 The dataset includes 243 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057287-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dqcmny
title: Occurrence Download

description: A dataset containing 103 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Abies cilicica (Antoine & Kotschy) Carrière",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 103 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039211-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ecqa5a
title: Occurrence Download

description: A dataset containing 3473 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Caprimulgus aegyptius M.H.K.Lichtenstein, 1823"
 ]
}

 The dataset includes 3473 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057254-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bfqevx
title: Occurrence Download

description: A dataset containing 158 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((28.26934 -26.47134,30.02792 -26.47134,30.02792 -25.76822,28.26934 -25.76822,28.26934 -26.47134))",
 "HasCoordinate is true",
 "TaxonKey is Actinopterygii",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 158 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039212-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p363bp
title: Occurrence Download

description: A dataset containing 24971 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Swiss National Databank of Vascular Plants",
 "Geometry POLYGON((10.22569 46.72648,10.41083 46.72648,10.41083 46.82621,10.22569 46.82621,10.22569 46.72648))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 24971 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0105291-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3j739y
title: Occurrence Download

description: A dataset containing 91 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Begonia serratipetala Irmsch."
 ]
}

 The dataset includes 91 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057255-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jtd5xl
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((74.7345 27.05913,74.85535 26.75542,75.31677 26.86328,75.09705 27.21556,74.7345 27.05913))",
 "HasCoordinate is true",
 "TaxonKey is Phoeniconaias minor (É.Geoffroy Saint-Hilaire, 1798)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 7 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039213-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kgg754
title: Occurrence Download

description: A dataset containing 751374 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 {
 "or" : [
 "Country is Canada",
 "Country is United States of America"
 ]
 },
 "Geometry POLYGON((-132.89062 48.63291,-125.2002 43.61222,-121.99219 45.27489,-121.11328 48.5166,-127.83691 56.29216,-135.04395 59.95501,-139.04297 59.84481,-140.27344 58.49369,-132.89062 48.63291))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 751374 records from 277 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0114788-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f7k9yp
title: Occurrence Download

description: A dataset containing 7443 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Synallaxis candei Orbigny & Lafresnaye, 1838"
 ]
}

 The dataset includes 7443 records from 71 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057345-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2atvni
title: Occurrence Download

description: A dataset containing 1791 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Salix laggeri Wimm."
 ]
}

 The dataset includes 1791 records from 39 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039214-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ww2v9k
title: Occurrence Download

description: A dataset containing 160 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hieracium lainzii de Retz",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 160 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002556-240130105604617/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j48vvj
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Blepharis tetrasticha Lindau"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057329-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.knv3xk
title: Occurrence Download

description: A dataset containing 230 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "TaxonKey is Callistus lunatus (Fabricius, 1775)",
 "TaxonKey is Callitriche deflexa A.Braun ex Hegelm."
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 230 records from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039215-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fpczc9
title: Occurrence Download

description: A dataset containing 1896 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Canada",
 "DatasetKey is iNaturalist Research-grade Observations",
 "TaxonKey is Ursus americanus Pallas, 1780",
 "Year 2010-2019"
 ]
}

 The dataset includes 1896 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0197865-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cql0ft
title: Occurrence Download

description: A dataset containing 1566720 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is Myanmar",
 "Country is Thailand",
 "Country is Cambodia",
 "Country is Viet Nam",
 "Country is Lao People’s Democratic Republic",
 "Country is Malaysia",
 "Country is Indonesia",
 "Country is Brunei Darussalam",
 "Country is Philippines"
 ]
 },
 "DatasetKey is EOD – eBird Observation Dataset"
 ]
}

 The dataset includes 1566720 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039217-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nrt3mu
title: Occurrence Download

description: A dataset containing 125 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Otus beccarii (Salvadori, 1876)"
 ]
}

 The dataset includes 125 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057332-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z33q5p
title: Occurrence Download

description: A dataset containing 340 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Stipa bungeana Trin."
 ]
}

 The dataset includes 340 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0096965-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.svaqx7
title: Occurrence Download

description: A dataset containing 51 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Blepharis transvaalensis Schinz"
 ]
}

 The dataset includes 51 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057347-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tetdvn
title: Occurrence Download

description: A dataset containing 3060 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "TaxonKey is Callidium violaceum (Linnaeus, 1758)"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 3060 records from 77 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039218-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8ram3f
title: Occurrence Download

description: A dataset containing 51427 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Phoradendron Nutt."
 ]
}

 The dataset includes 51427 records from 415 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0135394-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.abr2dp
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Blepharis uzondoensis Vollesen"
 ]
}

 The dataset includes 8 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057383-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dirgpb
title: Occurrence Download

description: A dataset containing 241 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Sweden",
 "HasCoordinate is true",
 "TaxonKey is Pipistrellus pipistrellus (Schreber, 1774)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 241 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039220-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8z78cd
title: Occurrence Download

description: A dataset containing 7172 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Specimen",
 "BasisOfRecord is Living Specimen"
 ]
 },
 "Continent is North America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Spinus tristis (Linnaeus, 1758)"
 ]
}

 The dataset includes 7172 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0129599-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.1p0ptp
title: Occurrence Download

description: A dataset containing 636293 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Amphipoda"
 ]
}

 The dataset includes 636293 records from 840 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039224-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9nty7p
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Accipitriformes)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1980",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Geometry POLYGON((-150 0,-120 0,-120 30,-150 30,-150 0))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0061513-250920141307145/datasets/export for details.
DOI: 10.15468/dl.umg5rx
title: Occurrence Download

description: A dataset containing 12271920 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 12271920 records from 2029 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000491-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15176026
title: Molecular insights on the pre-reactive complex between SHAPE probe and RNA molecules and its role in the SHAPE reaction: a multiscale study

description: Supporting Information for "Molecular insights on the pre-reactive complex between SHAPE probe and RNA molecules and its role in the SHAPE reaction: a multiscale study" by C. Hognon, A. Ben Abdeljaoued, P. Hardouin, M. Etheve-Quelquejeu, B. Sargueuil, D. Laage, E. Frezza.

We focused on the Bacillus subtilis yitJ S box/SAM-I riboswitch RNA, whose structure is available under PDB ID: 4KQY. The RNA was described using the Amber 99SB-ILDN force field with the BSC0 and χOL3 modifications.

All-atom MD simulations were conducted on both the isolated P3a stem-loop and the full RNA structure using GROMACS. The file start.pdb can be used to open the trajectories as the topology file. The plain MD simulations are available in the folder named AA. Each folder contains three repeats:





rep1 (ld-seed: -405291154 for the full structure and -1633222772 for the isolated stem-loop),




rep2 (ld-seed: -135266566 for the full structure and -1392585889 for the isolated stem-loop),




rep3 (ld-seed: -553742348 for the full structure and -419463185 for the isolated stem-loop).



In the folders 1DUS and 2DUS, we concatenated the simulations for each window and deposited the resulting trajectory for each nucleotide under investigation. 





In 1D US all-atom MD simulations, the collective variable is defined as the distance between the reactive carbon (C*) and the hydroxyl oxygen.




In 2D US all-atom MD simulations, we also included the angle α, defined by atoms C*, C4’, and C2’.



 

1D US QM-MM Simulations

The 1D US QM-MM simulations were performed using the AMBER software.

Amber Input FilesUmbrella sampling input files for the window at CV = 4 Å are provided as an example.

Trajectory VisualizationTo visualize the trajectories, use the provided topology file.

Topology





start.pdb: PDB file from the last frame of the production run at CV = 4 Å for αᵢ = 30°, used as the topology to open the trajectories.



Trajectories



all_noWAT_*.xtc:  concatenated windows from CV = 4 Å to CV = 1 Å of overall 61 windows of 250 ps each (625 frames per window) without ions and water molecules.

all_noWAT_30.xtc: trajectory for αi at 30°

all_noWAT_60.xtc: trajectory for αi  at 60°

all_noWAT_80.xtc: trajectory for αi at 80°
DOI: 10.5281/zenodo.15176027
title: Molecular insights on the pre-reactive complex between SHAPE probe and RNA molecules and its role in the SHAPE reaction: a multiscale study

description: Supporting Information for "Molecular insights on the pre-reactive complex between SHAPE probe and RNA molecules and its role in the SHAPE reaction: a multiscale study" by C. Hognon, A. Ben Abdeljaoued, P. Hardouin, M. Etheve-Quelquejeu, B. Sargueuil, D. Laage, E. Frezza.

We focused on the Bacillus subtilis yitJ S box/SAM-I riboswitch RNA, whose structure is available under PDB ID: 4KQY. The RNA was described using the Amber 99SB-ILDN force field with the BSC0 and χOL3 modifications.

All-atom MD simulations were conducted on both the isolated P3a stem-loop and the full RNA structure using GROMACS. The file start.pdb can be used to open the trajectories as the topology file. The plain MD simulations are available in the folder named AA. Each folder contains three repeats:





rep1 (ld-seed: -405291154 for the full structure and -1633222772 for the isolated stem-loop),




rep2 (ld-seed: -135266566 for the full structure and -1392585889 for the isolated stem-loop),




rep3 (ld-seed: -553742348 for the full structure and -419463185 for the isolated stem-loop).



In the folders 1DUS and 2DUS, we concatenated the simulations for each window and deposited the resulting trajectory for each nucleotide under investigation. 





In 1D US all-atom MD simulations, the collective variable is defined as the distance between the reactive carbon (C*) and the hydroxyl oxygen.




In 2D US all-atom MD simulations, we also included the angle α, defined by atoms C*, C4’, and C2’.



 

1D US QM-MM Simulations

The 1D US QM-MM simulations were performed using the AMBER software.

Amber Input FilesUmbrella sampling input files for the window at CV = 4 Å are provided as an example.

Trajectory VisualizationTo visualize the trajectories, use the provided topology file.

Topology





start.pdb: PDB file from the last frame of the production run at CV = 4 Å for αᵢ = 30°, used as the topology to open the trajectories.



Trajectories



all_noWAT_*.xtc:  concatenated windows from CV = 4 Å to CV = 1 Å of overall 61 windows of 250 ps each (625 frames per window) without ions and water molecules.

all_noWAT_30.xtc: trajectory for αi at 30°

all_noWAT_60.xtc: trajectory for αi  at 60°

all_noWAT_80.xtc: trajectory for αi at 80°
DOI: 10.13145/bacdive127333.20230509.8.1
title: Kitasatospora aureofaciens

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive127333.20251217.10
title: Kitasatospora aureofaciens

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive127334.20230509.8.1
title: Kitasatospora aureofaciens

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive127334.20251217.10
title: Kitasatospora aureofaciens

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive127335.20230509.8.1
title: Kitasatospora aureofaciens

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive127335.20251217.10
title: Kitasatospora aureofaciens

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive127336.20230509.8.1
title: Kitasatospora aureofaciens

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive127336.20251217.10
title: Kitasatospora aureofaciens

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive127337.20230509.8.1
title: Kitasatospora aureofaciens

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive127337.20251217.10
title: Kitasatospora aureofaciens

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive127338.20230509.8.1
title: Kitasatospora aureofaciens

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive127338.20251217.10
title: Kitasatospora aureofaciens

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive127339.20230509.8.1
title: Kitasatospora aureofaciens

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive127339.20251217.10
title: Kitasatospora aureofaciens

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive127340.20230509.8.1
title: Kitasatospora aureofaciens

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.