cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.3535/y8s-beh-8w5
title: Spiroloculina nitida d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/68h-wgl-kgy
title: Duvalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ddx-rhz-q62
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/qlz-gx6-4xp
title: Ammotium cassis (Parker, 1870)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/70p-1v6-268
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/w8z-kqs-keq
title: Duvalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/7nl-567-8tw
title: Terebratula Müller, 1776

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/hkw-bme-n6m
title: †Pseudohastigerina micra (Cole, 1927)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/zjm-5bl-z8d
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/6l4-egp-hrg
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/w0h-8nx-r44
title: †Ammonoidea

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/7wj-x1c-317
title: †Belemnitida

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/mvx-ngq-9bp
title: †Neolissoceras grasianus (d'Orbigny, 1841)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/alm-gz2-xee
title: †Belemnitida

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/d8j-szr-ba1
title: †Himantoceras trinodosum Thieuloy, 1965

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/55x-8af-c1k
title: Cytheretta jurinii (Muenster, 1830)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/c3g-he9-da4
title: †Cladiscites crassestriatus (von Mojsisovics, 1873)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/1j9-arg-s4h
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/sac-axa-t6r
title: †Belemnitida

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/apr-s8j-5zx
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/8s1-74s-52h
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/q62-wky-skh
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/88g-rlh-90q
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/f1m-q06-v32
title: Cytheropteron rotundatum Müller, 1894

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/mbr-53l-s29
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/nsq-ayk-4mc
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ens-vp8-ycb
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ljl-rpq-nw6
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/y67-jvb-p1w
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.15468/dl.2u27uf
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pleioblastus fortunei",
 "Country is Algeria",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020577-250811113504898/datasets/export for details.
DOI: 10.3535/a6c-m2s-3rd
title: †Camptocythere parvula Plumhoff, 1963

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/mlz-lq3-ekc
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.26093/cds/vizier.75124464
title: OpC study with UBVRI and Gaia EDR3

description: VizieR online Data Catalogue associated with article published in journal Monthly Notices of the Royal Astronomical Society with title ' 58 open clusters investigated with UBVRI and Gaia EDR3 data.' (bibcode: 2022MNRAS.512.4464D)
DOI: 10.3535/6b6-7ns-776
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/elv-8w3-jqb
title: †Acratia Delo, 1930

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/948-by0-4pq
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/mb9-vd2-h3z
title: Duvalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.15468/dl.c69ua2
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pleioblastus fortunei",
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020578-250811113504898/datasets/export for details.
DOI: 10.3535/j3n-lhz-lls
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/0x3-4f7-mfd
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/9wq-9v3-s9q
title: Oolina borealis Loeblich & Tappan, 1954

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.15468/dl.g3gfxn
title: Occurrence Download

description: A dataset containing 41 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Crenicichla labrina)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 41 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0086759-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fs45w5
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Impatiens capensis",
 "Country is Japan",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0086760-250717081556266/datasets/export for details.
DOI: 10.15468/dl.vmt9xv
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cenchrus polystachios",
 "Country is Indonesia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 6 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0086761-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25574/22348
title: Chandra X-ray Observatory ObsId 22348

description: Chandra Observations of the HD61005 Star-Disk-ISM Wind Interaction System
DOI: 10.25574/22349
title: Chandra X-ray Observatory ObsId 22349

description: Chandra Observations of the HD61005 Star-Disk-ISM Wind Interaction System
DOI: 10.25574/22486
title: Chandra X-ray Observatory ObsId 22486

description: X-ray emission from Lyman emitting galaxies
DOI: 10.25574/22510
title: Chandra X-ray Observatory ObsId 22510

description: A LOCAL CHARACTERIZATION OF THE z 10 X-RAY RADIATION FIELD AND ITS EFFECTS ON EARLY IGM HEATING
DOI: 10.5281/zenodo.18714737
title: Datasets for "Exploring Conformational Transitions of RNA Dimers via Machine Learning Potentials"

description: Show affiliations



Description



Here, you can access the molecular dynamics trajectories for the PMD and TREMD simulations of ApA dimer, as well as the quantum-mechanical datasets generated to train the equivariant ML potentials.

ABSTRACT

RNA is a highly flexible biopolymer that adopts a wide range of conformations while forming well-defined structural motifs essential for its biological function. Elucidating these structure–function relationships therefore requires a thorough exploration of its conformational landscape. In this sense, all-atom molecular dynamics (AAMD) simulations provide a powerful framework for this purpose. However, current classical RNA force fields often suffer from limited transferability and inefficient sampling of transitions between stable states, particularly in moderately large RNA systems. To overcome similar limitations in biomolecular modeling, quantum-informed machine learning (ML) potentials have recently emerged as a promising alternative, offering improved accuracy and transferability compared to classical force fields. In this work, we assess the performance of ML potentials in the exploration of RNA conformational space. As a model system, we focus on the adenine–adenine dinucleoside monophosphate (ApA) dimer, a fundamental RNA building block. We generated an extensive quantum-mechanical (QM) dataset of physicochemical properties for ApA conformations obtained from temperature replica exchange molecular dynamics (TREMD) simulations. Despite its small size, the ApA dimer exhibits a complex energetic landscape with six well-defined conformational clusters in which quantum effects and solvent-mediated interactions play a crucial role. Using this dataset, we parameterized ML potentials built on the equivariant MACE architecture and informed by both ab initio and semi-empirical property data. The resulting potentials successfully reproduce key conformational features of the ApA system, including base stacking, sugar puckering, and backbone flexibility. Moreover, they provide broader coverage of relevant structural transitions compared to the general-purpose SO3LR and MACE-OFF24 models. These findings underscore the importance of comprehensive QM datasets for RNA building blocks and highlight the need for robust and efficient validation metrics for assessing the performance of ML potentials.

PREPRINT

https://www.biorxiv.org/content/10.64898/2026.02.25.707885v1 

FILES:

dft_data.xz: quantum-mechanical data of ApA conformations computed at PBE0+MBD level.

dftb_dat.xz: quantum-mechanical data of ApA conformations computed at DFTB3+MBD level.

plainMD.xz: MD trajectory of solvated ApA dimer at constant temperature.

tremd.xz: TREMD trajectory of solvated ApA dimer.

MLmodels.xz: ML potentials developed in this work.

dihedral_transitions.xz: Scripts for the structural analysis and conformational classification of MD trajectories.
DOI: 10.5281/zenodo.18714738
title: Datasets for "Exploring Conformational Transitions of RNA Dimers via Machine Learning Potentials"

description: Show affiliations



Description



Here, you can access the molecular dynamics trajectories for the PMD and TREMD simulations of ApA dimer, as well as the quantum-mechanical datasets generated to train the equivariant ML potentials.

ABSTRACT

RNA is a highly flexible biopolymer that adopts a wide range of conformations while forming well-defined structural motifs essential for its biological function. Elucidating these structure–function relationships therefore requires a thorough exploration of its conformational landscape. In this sense, all-atom molecular dynamics (AAMD) simulations provide a powerful framework for this purpose. However, current classical RNA force fields often suffer from limited transferability and inefficient sampling of transitions between stable states, particularly in moderately large RNA systems. To overcome similar limitations in biomolecular modeling, quantum-informed machine learning (ML) potentials have recently emerged as a promising alternative, offering improved accuracy and transferability compared to classical force fields. In this work, we assess the performance of ML potentials in the exploration of RNA conformational space. As a model system, we focus on the adenine–adenine dinucleoside monophosphate (ApA) dimer, a fundamental RNA building block. We generated an extensive quantum-mechanical (QM) dataset of physicochemical properties for ApA conformations obtained from temperature replica exchange molecular dynamics (TREMD) simulations. Despite its small size, the ApA dimer exhibits a complex energetic landscape with six well-defined conformational clusters in which quantum effects and solvent-mediated interactions play a crucial role. Using this dataset, we parameterized ML potentials built on the equivariant MACE architecture and informed by both ab initio and semi-empirical property data. The resulting potentials successfully reproduce key conformational features of the ApA system, including base stacking, sugar puckering, and backbone flexibility. Moreover, they provide broader coverage of relevant structural transitions compared to the general-purpose SO3LR and MACE-OFF24 models. These findings underscore the importance of comprehensive QM datasets for RNA building blocks and highlight the need for robust and efficient validation metrics for assessing the performance of ML potentials.

PREPRINT

https://www.biorxiv.org/content/10.64898/2026.02.25.707885v1 

FILES:

dft_data.xz: quantum-mechanical data of ApA conformations computed at PBE0+MBD level.

dftb_dat.xz: quantum-mechanical data of ApA conformations computed at DFTB3+MBD level.

plainMD.xz: MD trajectory of solvated ApA dimer at constant temperature.

tremd.xz: TREMD trajectory of solvated ApA dimer.

MLmodels.xz: ML potentials developed in this work.

dihedral_transitions.xz: Scripts for the structural analysis and conformational classification of MD trajectories.
DOI: 10.15468/dl.3bryqm
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "DistanceFromCentroidInMeters is greater than or equal to 2000",
 "Geometry POLYGON ((105.610544 14.999999, 179.999961 14.999999, 179.999961 65.08290100000001, 105.610544 65.08290100000001, 105.610544 14.999999))",
 "TaxonKey is Oplegnathus peaolopesi"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001549-260226173443078/datasets/export for details.
DOI: 10.6084/m9.figshare.30578309
title: The genomic assembly and annotation results of Chaetoceros socialis

description: The first chromosome-level genome assembly of the Chaetoceros socialis
DOI: 10.6084/m9.figshare.30578309.v1
title: The genomic assembly and annotation results of Chaetoceros socialis

description: The first chromosome-level genome assembly of the Chaetoceros socialis
DOI: 10.15468/dl.pafxnu
title: Occurrence Download

description: A dataset containing 532 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Saxifraga tricuspidata",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 532 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001548-260226173443078/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.czrm62
title: Occurrence Download

description: A dataset containing 68 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sus cebifrons"
 ]
}

 The dataset includes 68 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001550-260226173443078/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.46hse8
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eudiscoderma thongareeae"
 ]
}

 The dataset includes 9 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001551-260226173443078/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18798538
title: Importance of Cybersecurity Competences

description: Results from a survey performed among Slovenian companies on which Cybersecurity competences/skills they find the most important for their organization's work.
DOI: 10.5281/zenodo.18798537
title: Importance of Cybersecurity Competences

description: Results from a survey performed among Slovenian companies on which Cybersecurity competences/skills they find the most important for their organization's work.
DOI: 10.15468/dl.tw5gbf
title: Occurrence Download

description: A dataset containing 93 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "DistanceFromCentroidInMeters is greater than or equal to 2000",
 "Geometry POLYGON ((105.610544 14.999999, 179.999961 14.999999, 179.999961 65.08290100000001, 105.610544 65.08290100000001, 105.610544 14.999999))",
 "TaxonKey is Histiopterus typus"
 ]
}

 The dataset includes 93 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001552-260226173443078/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.56bycq
title: Occurrence Download

description: A dataset containing 323 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Chamaerhodos erecta",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 323 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001553-260226173443078/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34810/data1707
title: Informe Del Análisis Antracológico De Los Yacimientos De La Sendilla (Cienpozuelos), El Colegio (Valdemoro), Buzanca y La Recomba (Leganés)

description: Anthracological data from the rescue excavations at Buzanca 1 (Cienpozuelos, Madrid).
The attached data come from the anthracological record from a Chalcolithic site.
DOI: 10.5281/zenodo.18798541
title: Open Data Culturally EI Paper 1 2025
DOI: 10.5281/zenodo.18798542
title: Open Data Culturally EI Paper 1 2025
DOI: 10.5281/zenodo.18798518
title: THE IMPACT OF ADOLESCENTS' PSYCHOLOGICAL LITERACY ON THEIR ACADEMIC ACHIEVEMENT

description: This article examines the impact of psychological literacy on adolescents’ academic achievement. Psychological literacy is considered an essential component of personal development, emotional regulation, and effective learning behavior. The study highlights the relationship between students’ awareness of psychological processes, their ability to manage emotions, motivation, and academic performance. The findings suggest that higher levels of psychological literacy positively influence learning outcomes, self-regulation, and educational engagement among adolescents.
DOI: 10.5281/zenodo.18798519
title: THE IMPACT OF ADOLESCENTS' PSYCHOLOGICAL LITERACY ON THEIR ACADEMIC ACHIEVEMENT

description: This article examines the impact of psychological literacy on adolescents’ academic achievement. Psychological literacy is considered an essential component of personal development, emotional regulation, and effective learning behavior. The study highlights the relationship between students’ awareness of psychological processes, their ability to manage emotions, motivation, and academic performance. The findings suggest that higher levels of psychological literacy positively influence learning outcomes, self-regulation, and educational engagement among adolescents.
DOI: 10.15468/dl.cwjpx3
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "DistanceFromCentroidInMeters is greater than or equal to 2000",
 "Geometry POLYGON ((105.610544 14.999999, 179.999961 14.999999, 179.999961 65.08290100000001, 105.610544 65.08290100000001, 105.610544 14.999999))",
 "TaxonKey is Pentaceros capensis"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001555-260226173443078/datasets/export for details.
DOI: 10.15468/dl.qqezu7
title: Occurrence Download

description: A dataset containing 996 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Linum lewisii",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 996 records from 98 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001556-260226173443078/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.