cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.26404523.v1
title: A SAR and QSAR study on 3CLpro inhibitors of SARS-CoV-2 using machine learning methods

description: The 3C-like Proteinase (3CLpro) of novel coronaviruses is intricately linked to viral replication, making it a crucial target for antiviral agents. In this study, we employed two fingerprint descriptors (ECFP_4 and MACCS) to comprehensively characterize 889 compounds in our dataset. We constructed 24 classification models using machine learning algorithms, including Support Vector Machine (SVM), Random Forest (RF), extreme Gradient Boosting (XGBoost), and Deep Neural Networks (DNN). Among these models, the DNN- and ECFP_4-based Model 1D_2 achieved the most promising results, with a remarkable Matthews correlation coefficient (MCC) value of 0.796 in the 5-fold cross-validation and 0.722 on the test set. The application domains of the models were analysed using d<sub>STD-PRO</sub> calculations. The collected 889 compounds were clustered by K-means algorithm, and the relationships between structural fragments and inhibitory activities of the highly active compounds were analysed for the 10 obtained subsets. In addition, based on 464 3CLpro inhibitors, 27 QSAR models were constructed using three machine learning algorithms with a minimum root mean square error (RMSE) of 0.509 on the test set. The applicability domains of the models and the structure-activity relationships responded from the descriptors were also analysed.
DOI: 10.6084/m9.figshare.26404523
title: A SAR and QSAR study on 3CLpro inhibitors of SARS-CoV-2 using machine learning methods

description: The 3C-like Proteinase (3CLpro) of novel coronaviruses is intricately linked to viral replication, making it a crucial target for antiviral agents. In this study, we employed two fingerprint descriptors (ECFP_4 and MACCS) to comprehensively characterize 889 compounds in our dataset. We constructed 24 classification models using machine learning algorithms, including Support Vector Machine (SVM), Random Forest (RF), extreme Gradient Boosting (XGBoost), and Deep Neural Networks (DNN). Among these models, the DNN- and ECFP_4-based Model 1D_2 achieved the most promising results, with a remarkable Matthews correlation coefficient (MCC) value of 0.796 in the 5-fold cross-validation and 0.722 on the test set. The application domains of the models were analysed using d<sub>STD-PRO</sub> calculations. The collected 889 compounds were clustered by K-means algorithm, and the relationships between structural fragments and inhibitory activities of the highly active compounds were analysed for the 10 obtained subsets. In addition, based on 464 3CLpro inhibitors, 27 QSAR models were constructed using three machine learning algorithms with a minimum root mean square error (RMSE) of 0.509 on the test set. The applicability domains of the models and the structure-activity relationships responded from the descriptors were also analysed.
DOI: 10.6084/m9.figshare.26495175
title: Essential oil components interacting with insect odorant-binding proteins: a molecular modelling approach

description: Essential oils (EOs) are natural products currently used to control arthropods, and their interaction with insect odorant-binding proteins (OBPs) is fundamental for the discovery of new repellents. This in silico study aimed to predict the potential of EO components to interact with odorant proteins. A total of 684 EO components from PubChem were docked against 23 odorant binding proteins from Protein Data Bank using AutoDock Vina. The ligands and proteins were optimized using Gaussian 09 and Sybyl-X 2.0, respectively. The nature of the protein-ligand interactions was characterized using LigandScout 4.0, and visualization of the binding mode in selected complexes was carried out by Pymol. Additionally, complexes with the best binding energy in molecular docking were subjected to 500 ns molecular dynamics simulations using Gromacs. The best binding affinity values were obtained for the 1DQE-ferutidine (−11 kcal/mol) and 2WCH-kaurene (−11.2 kcal/mol) complexes. Both are natural ligands that dock onto those proteins at the same binding site as DEET, a well-known insect repellent. This study identifies kaurene and ferutidine as possible candidates for natural insect repellents, offering a potential alternative to synthetic chemicals like DEET.
DOI: 10.6084/m9.figshare.26495175.v1
title: Essential oil components interacting with insect odorant-binding proteins: a molecular modelling approach

description: Essential oils (EOs) are natural products currently used to control arthropods, and their interaction with insect odorant-binding proteins (OBPs) is fundamental for the discovery of new repellents. This in silico study aimed to predict the potential of EO components to interact with odorant proteins. A total of 684 EO components from PubChem were docked against 23 odorant binding proteins from Protein Data Bank using AutoDock Vina. The ligands and proteins were optimized using Gaussian 09 and Sybyl-X 2.0, respectively. The nature of the protein-ligand interactions was characterized using LigandScout 4.0, and visualization of the binding mode in selected complexes was carried out by Pymol. Additionally, complexes with the best binding energy in molecular docking were subjected to 500 ns molecular dynamics simulations using Gromacs. The best binding affinity values were obtained for the 1DQE-ferutidine (−11 kcal/mol) and 2WCH-kaurene (−11.2 kcal/mol) complexes. Both are natural ligands that dock onto those proteins at the same binding site as DEET, a well-known insect repellent. This study identifies kaurene and ferutidine as possible candidates for natural insect repellents, offering a potential alternative to synthetic chemicals like DEET.
DOI: 10.6084/m9.figshare.26935839
title: Combining QSAR and SSD to predict aquatic toxicity and species sensitivity of pyrethroid and organophosphate pesticides

description: The widespread use of pyrethroid and organophosphate pesticides necessitates accurate toxicity predictions for regulatory compliance. In this study QSAR and SSD models for six pyrethroid and four organophosphate compounds using QSAR Toolbox and SSD Toolbox have been developed. The QSAR models, described by the formula 48 h-EC50 or 96 h-LC50 = x + y * log Kow, were validated for predicting 48 h-EC50 values for acute <i>Daphnia</i> toxicity and 96 h-LC50 values for acute fish toxicity, meeting criteria of <i>n</i> ≥10, <i>r</i><sup>2</sup> ≥0.7, and <i>Q</i><sup>2</sup> &gt;0.5. Predicted 48 h-EC50 values for pyrethroids ranged from 3.95 × 10<sup>−5</sup> mg/L (permethrin) to 8.21 × 10<sup>−3</sup> mg/L (fenpropathrin), and 96 h-LC50 values from 3.89 × 10<sup>−5</sup> mg/L (permethrin) to 1.68 × 10<sup>−2</sup> mg/L (metofluthrin). For organophosphates, 48 h-EC50 values ranged from 2.00 × 10<sup>−5</sup> mg/L (carbophenothion) to 3.76 × 10<sup>−2</sup> mg/L (crufomate) and 96 h-LC50 values from 3.81 × 10<sup>−3</sup> mg/L (carbophenothion) to 12.3 mg/L (crufomate). These values show a good agreement with experimental data, though some, like Carbophenothion, overestimated toxicity. HC05 values, indicating hazardous concentrations for 5% of species, range from 0.029 to 0.061 µg/L for pyrethroids and 0.030 to 0.072 µg/L for organophosphates. These values aid in establishing environmental quality standards (EQS). Compared to existing EQS, HC05 values for pyrethroids were less conservative, while those for organophosphates were comparable.
DOI: 10.6084/m9.figshare.26935839.v2
title: Combining QSAR and SSD to predict aquatic toxicity and species sensitivity of pyrethroid and organophosphate pesticides

description: The widespread use of pyrethroid and organophosphate pesticides necessitates accurate toxicity predictions for regulatory compliance. In this study QSAR and SSD models for six pyrethroid and four organophosphate compounds using QSAR Toolbox and SSD Toolbox have been developed. The QSAR models, described by the formula 48 h-EC50 or 96 h-LC50 = x + y * log Kow, were validated for predicting 48 h-EC50 values for acute <i>Daphnia</i> toxicity and 96 h-LC50 values for acute fish toxicity, meeting criteria of <i>n</i> ≥10, <i>r</i><sup>2</sup> ≥0.7, and <i>Q</i><sup>2</sup> &gt;0.5. Predicted 48 h-EC50 values for pyrethroids ranged from 3.95 × 10<sup>−5</sup> mg/L (permethrin) to 8.21 × 10<sup>−3</sup> mg/L (fenpropathrin), and 96 h-LC50 values from 3.89 × 10<sup>−5</sup> mg/L (permethrin) to 1.68 × 10<sup>−2</sup> mg/L (metofluthrin). For organophosphates, 48 h-EC50 values ranged from 2.00 × 10<sup>−5</sup> mg/L (carbophenothion) to 3.76 × 10<sup>−2</sup> mg/L (crufomate) and 96 h-LC50 values from 3.81 × 10<sup>−3</sup> mg/L (carbophenothion) to 12.3 mg/L (crufomate). These values show a good agreement with experimental data, though some, like Carbophenothion, overestimated toxicity. HC05 values, indicating hazardous concentrations for 5% of species, range from 0.029 to 0.061 µg/L for pyrethroids and 0.030 to 0.072 µg/L for organophosphates. These values aid in establishing environmental quality standards (EQS). Compared to existing EQS, HC05 values for pyrethroids were less conservative, while those for organophosphates were comparable.
DOI: 10.6084/m9.figshare.26935839.v1
title: Combining QSAR and SSD to predict aquatic toxicity and species sensitivity of pyrethroid and organophosphate pesticides

description: The widespread use of pyrethroid and organophosphate pesticides necessitates accurate toxicity predictions for regulatory compliance. In this study QSAR and SSD models for six pyrethroid and four organophosphate compounds using QSAR Toolbox and SSD Toolbox have been developed. The QSAR models, described by the formula 48 h-EC50 or 96 h-LC50 = x + y * log Kow, were validated for predicting 48 h-EC50 values for acute <i>Daphnia</i> toxicity and 96 h-LC50 values for acute fish toxicity, meeting criteria of <i>n</i> ≥10, <i>r</i><sup>2</sup> ≥0.7, and <i>Q</i><sup>2</sup> &gt;0.5. Predicted 48 h-EC50 values for pyrethroids ranged from 3.95 × 10<sup>−5</sup> mg/L (permethrin) to 8.21 × 10<sup>−3</sup> mg/L (fenpropathrin), and 96 h-LC50 values from 3.89 × 10<sup>−5</sup> mg/L (permethrin) to 1.68 × 10<sup>−2</sup> mg/L (metofluthrin). For organophosphates, 48 h-EC50 values ranged from 2.00 × 10<sup>−5</sup> mg/L (carbophenothion) to 3.76 × 10<sup>−2</sup> mg/L (crufomate) and 96 h-LC50 values from 3.81 × 10<sup>−3</sup> mg/L (carbophenothion) to 12.3 mg/L (crufomate). These values show a good agreement with experimental data, though some, like Carbophenothion, overestimated toxicity. HC05 values, indicating hazardous concentrations for 5% of species, range from 0.029 to 0.061 µg/L for pyrethroids and 0.030 to 0.072 µg/L for organophosphates. These values aid in establishing environmental quality standards (EQS). Compared to existing EQS, HC05 values for pyrethroids were less conservative, while those for organophosphates were comparable.
DOI: 10.5281/zenodo.13737007
title: Eutin Sonnen-Apotheke (ca. 1924/47)

description: Historical questionnaire/s 1924/1948 and index cards, partly selected enclosures regarding the history of a German pharmacy, catalogued via Kalliope portal (Historischer Fragebogen 1924/1948 und Karteikarten, ggf. gemeinfreie Anlagen zur Apothekengeschichte; als Katalog dient das Nachlassportal Kalliope): https://kalliope-verbund.info/DE-611-BF-70963 [Funktion: Im Findbuch anzeigen]Please note: The Kalliope catalogue entry might indicate related material in the archival folder which cannot be published due to copyright or other legal restrictions (NB: Das Katalogisat bei Kalliope kann auch auf Materialien - teils erheblichen Umfangs - verweisen, die aus archiv- oder urheberrechtlichen Gründen nicht veröffentlicht werden dürfen).
DOI: 10.25921/qrtx-n896
title: 2012-2014 Deep Sea Coral and Sponge Aleutian Islands DropCam Survey
DOI: 10.15468/dl.gtywhm
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Pseudoeurycea aurantia Canseco-Márquez & Parra-Olea, 2003)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 17 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008181-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4458a8
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Cnemaspis latha Manamendra-Arachchi, Batuwita & Pethiyagoda, 2007, Cnemaspis pava Manamendra-Arachchi, Batuwita & Pethiyagoda, 2007)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 5 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008182-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xuhdhd
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Chilabothrus granti (Stull, 1933))",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 10 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008183-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k9zy4n
title: Occurrence Download

description: A dataset containing 2259 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Crypteroniaceae"
 ]
}

 The dataset includes 2259 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008184-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s8rstt
title: Occurrence Download

description: A dataset containing 40 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Pseudoeurycea orchimelas (Brodie, Mendelson & Campbell, 2002), Pseudoeurycea orchimela (Brodie, Mendelson & Campbell, 2002))",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 40 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008186-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nbhruz
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Cnemaspis kumarasinghei Mendis Wickramasinghe & Munindradasa, 2007)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 5 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008187-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2mamyn
title: Occurrence Download

description: A dataset containing 47 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Chioninia vaillantii (Boulenger, 1887))",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 47 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008188-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13737039
title: Eutingen Apotheke (ca. 1924/47)

description: Historical questionnaire/s 1924/1948 and index cards, partly selected enclosures regarding the history of a German pharmacy, catalogued via Kalliope portal (Historischer Fragebogen 1924/1948 und Karteikarten, ggf. gemeinfreie Anlagen zur Apothekengeschichte; als Katalog dient das Nachlassportal Kalliope): https://kalliope-verbund.info/DE-611-BF-70963 [Funktion: Im Findbuch anzeigen]Please note: The Kalliope catalogue entry might indicate related material in the archival folder which cannot be published due to copyright or other legal restrictions (NB: Das Katalogisat bei Kalliope kann auch auf Materialien - teils erheblichen Umfangs - verweisen, die aus archiv- oder urheberrechtlichen Gründen nicht veröffentlicht werden dürfen).
DOI: 10.15468/dl.c6fa4p
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Cnemaspis kallima Manamendra-Arachchi, Batuwita & Pethiyagoda, 2007)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 4 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008190-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.adw6y8
title: Occurrence Download

description: A dataset containing 45 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Pseudoeurycea papenfussi Parra-Olea, García-París, Hanken & Wake, 2005)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 45 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008189-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cpm3ab
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Bitis parviocula Böhme, 1976)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 11 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008191-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13737086
title: Eveking Engel-Apotheke (ca. 1924/47)

description: Historical questionnaire/s 1924/1948 and index cards, partly selected enclosures regarding the history of a German pharmacy, catalogued via Kalliope portal (Historischer Fragebogen 1924/1948 und Karteikarten, ggf. gemeinfreie Anlagen zur Apothekengeschichte; als Katalog dient das Nachlassportal Kalliope): https://kalliope-verbund.info/DE-611-BF-70963 [Funktion: Im Findbuch anzeigen]Please note: The Kalliope catalogue entry might indicate related material in the archival folder which cannot be published due to copyright or other legal restrictions (NB: Das Katalogisat bei Kalliope kann auch auf Materialien - teils erheblichen Umfangs - verweisen, die aus archiv- oder urheberrechtlichen Gründen nicht veröffentlicht werden dürfen).
DOI: 10.15468/dl.nx3cyw
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Cnemaspis gemunu Bauer, De Silva, Greenbaum & Jackman, 2007)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 5 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008192-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pwddcu
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Oedipina gephyra McCranie, Wilson & Williams, 1993)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 18 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008193-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zvbqtw
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Bitis worthingtoni Parker, 1932)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 13 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008194-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m2qdyh
title: Occurrence Download

description: A dataset containing 42 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is South Africa",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Pelophylax perezi (López-Seoane, 1885)"
 ]
}

 The dataset includes 42 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008197-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sqamsb
title: Occurrence Download

description: A dataset containing 695 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Alzateaceae"
 ]
}

 The dataset includes 695 records from 62 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008195-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m5sssg
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Bitis heraldica (Bocage, 1889))",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008200-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.