cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.11642744
title: modelforge curated dataset: ANI-2x

description: Curated ANI-2x Dataset:

Full dataset, version "full_dataset_v0":

This provides a curated hdf5 file for the ANI-2x dataset designed to be compatible with modelforge, an infrastructure to implement and train NNPs.  This dataset contains 9,651,712 total conformers, for 16514 unique entries (note, conformers are paritioned into entries based on the array of atomic species appearing in sequence in the source data file). 

When applicable, the units of properties are provided in the datafile,  encoded as strings compatible with the openff-units package.  For more information about the structure of the data file, please see the following:



https://github.com/choderalab/modelforge/wiki/Dataset-and-curation#curation-module


This curated dataset was generated using the modelforge software at commit c5c7153:



Link to the source code at this commit: https://github.com/choderalab/modelforge/tree/c5c7153e06172fe8e6f25015250ecb5db05655cc

Link to the script file used to generate the dataset: https://github.com/choderalab/modelforge/blob/c5c7153e06172fe8e6f25015250ecb5db05655cc/modelforge/curation/scripts/curate_spice2.py 


 

Source Dataset:



The ANI-2x data set includes properties for small organic molecules that contain H, C, N, O, S, F, and Cl. This dataset contains 9651712 conformers. This data was generated with the wB97X/631Gd level of theory used in the original ANI-2x paper, calculated using Gaussian 09.


Citations:

ANI-2x publication:







Devereux, C, Zubatyuk, R., Smith, J. et al. "Extending the applicability of the ANI deep learning molecular potential to sulfur and halogens." Journal of Chemical Theory and Computation 16.7 (2020): 4192-4202. https://doi.org/10.1021/acs.jctc.0c00121




Source dataset, released with CC Attribution 4.0 International license:



Huddleston, K., Zubatyuk, R., Smith, J., Roitberg, A., Isayev, O., Pickering, I., Devereux, C., & Barros, K. (2023). ANI-2x Release [Data set]. Zenodo. https://doi.org/10.5281/zenodo.10108942
DOI: 10.5281/zenodo.12059090
title: modelforge curated dataset: ANI-2x

description: Curated ANI-2x Dataset:

1000 conformer test set, version "nc_1000_v0":

This provides a curated hdf5 file for a subset of the ANI-2x dataset designed to be compatible with modelforge, an infrastructure to implement and train NNPs.  This dataset contains 1000 total conformers, for 101 unique entries, useful for testing (note, conformers are paritioned into entries based on the array of atomic species appearing in sequence in the source data file). 

When applicable, the units of properties are provided in the datafile,  encoded as strings compatible with the openff-units package.  For more information about the structure of the data file, please see the following:



https://github.com/choderalab/modelforge/wiki/Dataset-and-curation#curation-module


This curated dataset was generated using the modelforge software at commit c5c7153:



Link to the source code at this commit: https://github.com/choderalab/modelforge/tree/c5c7153e06172fe8e6f25015250ecb5db05655cc

Link to the script file used to generate the dataset: https://github.com/choderalab/modelforge/blob/c5c7153e06172fe8e6f25015250ecb5db05655cc/modelforge/curation/scripts/curate_spice2.py 


 

Source Dataset:



The ANI-2x data set includes properties for small organic molecules that contain H, C, N, O, S, F, and Cl. This dataset contains 9651712 conformers. This data was generated with the wB97X/631Gd level of theory used in the original ANI-2x paper, calculated using Gaussian 09.


Citations:

ANI-2x publication:







Devereux, C, Zubatyuk, R., Smith, J. et al. "Extending the applicability of the ANI deep learning molecular potential to sulfur and halogens." Journal of Chemical Theory and Computation 16.7 (2020): 4192-4202. https://doi.org/10.1021/acs.jctc.0c00121




Source dataset, released with CC Attribution 4.0 International license:



Huddleston, K., Zubatyuk, R., Smith, J., Roitberg, A., Isayev, O., Pickering, I., Devereux, C., & Barros, K. (2023). ANI-2x Release [Data set]. Zenodo. https://doi.org/10.5281/zenodo.10108942
DOI: 10.5281/zenodo.15346224
title: modelforge curated dataset: ANI-2x

description: Modelforge Curated ANI-2x Dataset:- full dataset- Version: full_dataset_v1.1

This provides a curated hdf5 file for the ANI-2x dataset designed to be compatible with modelforge, an infrastructure to implement and train NNPs. 

This dataset contains 16514 unique records for 9651712  total configurations.  Note, configurations are partitioned into entries based on the array of atomic species appearing in sequence in the source data file.

When applicable, the units of properties are provided in the datafile,  encoded as strings compatible with the openff-units package.  For more information about the structure of the data file, please see the following:

This dataset is compatible with modelforge hdf5 schema 2.

Properties Included:     



atomic_numbers 

positions       



"per_atom"

 "nanometer"



forces  



"per_atom"

 "kilojoule_per_mole / nanometer"



energies        



"per_system"

"kilojoule_per_mole"




Source Dataset:



The ANI-2x data set includes properties for small organic molecules that contain H, C, N, O, S, F, and Cl. This dataset contains 9651712 conformers. This data was generated with the wB97X/631Gd level of theory used in the original ANI-2x paper, calculated using Gaussian 09.


Citations:

ANI-2x publication:







Devereux, C, Zubatyuk, R., Smith, J. et al. "Extending the applicability of the ANI deep learning molecular potential to sulfur and halogens." Journal of Chemical Theory and Computation 16.7 (2020): 4192-4202. https://doi.org/10.1021/acs.jctc.0c00121




Source dataset, released with CC Attribution 4.0 International license:



Huddleston, K., Zubatyuk, R., Smith, J., Roitberg, A., Isayev, O., Pickering, I., Devereux, C., & Barros, K. (2023). ANI-2x Release [Data set]. Zenodo. https://doi.org/10.5281/zenodo.10108942
DOI: 10.5281/zenodo.15346340
title: modelforge curated dataset: ANI-2x

description: Modelforge Curated ANI-2x Dataset:- 1000 configuration test set- Version: nc_1000_v1.1

This provides a curated hdf5 file for a subset of the ANI-2x dataset designed to be compatible with modelforge, an infrastructure to implement and train NNPs.  This dataset contains 101 unique records for 1000  total configurations, with a maximum of 10 per system.   Note, configurations are parititioned into records based on the array of atomic species appearing in sequence in the source data file.

When applicable, the units of properties are provided in the datafile,  encoded as strings compatible with the openff-units package.  For more information about the structure of the data file, please see the following:

This dataset is compatible with modelforge hdf5 schema 2.

Properties Included:     



atomic_numbers 

positions       



"per_atom"

 "nanometer"



forces  



"per_atom"

 "kilojoule_per_mole / nanometer"



energies        



"per_system"

"kilojoule_per_mole"




Source Dataset:



The ANI-2x data set includes properties for small organic molecules that contain H, C, N, O, S, F, and Cl. This dataset contains 9651712 conformers. This data was generated with the wB97X/631Gd level of theory used in the original ANI-2x paper, calculated using Gaussian 09.


Citations:

ANI-2x publication:







Devereux, C, Zubatyuk, R., Smith, J. et al. "Extending the applicability of the ANI deep learning molecular potential to sulfur and halogens." Journal of Chemical Theory and Computation 16.7 (2020): 4192-4202. https://doi.org/10.1021/acs.jctc.0c00121




Source dataset, released with CC Attribution 4.0 International license:



Huddleston, K., Zubatyuk, R., Smith, J., Roitberg, A., Isayev, O., Pickering, I., Devereux, C., & Barros, K. (2023). ANI-2x Release [Data set]. Zenodo. https://doi.org/10.5281/zenodo.10108942
DOI: 10.3886/7j33-f574
title: Jordan Compact - Water Smart Homes: Final Analysis Report
DOI: 10.3886/zfy9-b672
title: Jordan Compact - Water Smart Homes: Final Analysis Report
DOI: 10.7294/28966283
title: Dataset associated with: Disease Signatures in Whole Plants and Callus Culture of <i>Arabidopsis thaliana</i> Infected with the Fungal Plant Pathogen <i>Fusarium graminearum</i>

description: This dataset accompanies the manuscript titled <i>"Disease Signatures in Whole Plants and Callus Culture of Arabidopsis thaliana Infected with the Fungal Plant Pathogen Fusarium graminearum"</i> by McMullan et al. (to be submitted to <i>Plant Cell, Tissue and Organ Culture</i>). It includes quantitative measurements related to fungal infection severity and mycotoxin production in both whole plants and callus cultures of <i>Arabidopsis thaliana</i>. Three <i>A. thaliana</i> accessions with documented differences in susceptibility were assessed at 7, 14, and 21 days post-inoculation. Each file includes metadata for accession identity, timepoint, biological replicate, and the specific metric of interest. These datasets support analysis of host response dynamics and enable comparisons between whole-plant and callus-based systems for modeling plant-pathogen interactions. The data may also inform future work on phytosensor development and fungal secondary metabolite detection in simplified in vitro systems.
DOI: 10.5281/zenodo.15390946
title: NIH 3T3 fibroblast stimulation by AcP2N3 to migrate

description: In vitro study done in collaboration with Università di Bologna, Italy. Results show a clear response by stimulated fibroblasts in comparison to controls.
DOI: 10.5281/zenodo.15390947
title: NIH 3T3 fibroblast stimulation by AcP2N3 to migrate

description: In vitro study done in collaboration with Università di Bologna, Italy. Results show a clear response by stimulated fibroblasts in comparison to controls.
DOI: 10.5281/zenodo.15376112
title: Application of Lossy Compression for MX Diffraction Data: use of lossy but not lossy compression (l_bnl_compress)

description: These are 3 data sets that are used to evaluate application of lossy compression for MX diffraction data. 

A lysosyme data set collected at 7500 eV to solve the S_SAD structure (Ly_01_22013). 

A thermolysin data set from a fragment screening campaign collection at the NSLS-II AMX beamline with a fragment bound (tlys-817_10982). 

A  CBASS Cap5 from Pseudomonas syringae as an activated tetramer with the cyclic dinucleotide 3'2'-c-diAMP ligand data set (Endo6_23AA_2v_502).

The CBASS Cap5 structure was published and deposited to the PDB site (8FMG.PDB and https://doi.org/10.1038/s41594-024-01220-x). 

The 7500 eV lysosyme structure was solved using S_SAD phases initial compression results are published (9B7F.PDB and https://doi.org/10.1107/S160057752400359X). 

 

For each data set, we include the corresponding XDS.INP file containing all metadata required for data reduction). 

 

We are grateful to Dr. Dale Kreitler (NSLS-II, BNL) for providing full access to the thermolysin data set. 

 

We are grateful to Dr. Olga Rechkoblit (MSSM) and Dr. Aneel Aggarwal (MSSM) for providing full access to the CBASS Cap5 data set.
DOI: 10.5281/zenodo.15376113
title: Application of Lossy Compression for MX Diffraction Data: use of lossy but not lossy compression (l_bnl_compress)

description: These are 3 data sets that are used to evaluate application of lossy compression for MX diffraction data. 

A lysosyme data set collected at 7500 eV to solve the S_SAD structure (Ly_01_22013). 

A thermolysin data set from a fragment screening campaign collection at the NSLS-II AMX beamline with a fragment bound (tlys-817_10982). 

A  CBASS Cap5 from Pseudomonas syringae as an activated tetramer with the cyclic dinucleotide 3'2'-c-diAMP ligand data set (Endo6_23AA_2v_502).

The CBASS Cap5 structure was published and deposited to the PDB site (8FMG.PDB and https://doi.org/10.1038/s41594-024-01220-x). 

The 7500 eV lysosyme structure was solved using S_SAD phases initial compression results are published (9B7F.PDB and https://doi.org/10.1107/S160057752400359X). 

 

For each data set, we include the corresponding XDS.INP file containing all metadata required for data reduction). 

 

We are grateful to Dr. Dale Kreitler (NSLS-II, BNL) for providing full access to the thermolysin data set. 

 

We are grateful to Dr. Olga Rechkoblit (MSSM) and Dr. Aneel Aggarwal (MSSM) for providing full access to the CBASS Cap5 data set.
DOI: 10.15468/dl.4kgvra
title: Occurrence Download

description: A dataset containing 665 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "IucnRedListCategory is one of (VU, EN, NT)",
 "OccurrenceStatus is Present",
 "TaxonKey is Chiroptera"
 ]
}

 The dataset includes 665 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026978-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15391764
title: data Asymmetric Impacts of the Energy Market on Stock Indexes in Emerging Economies: A Quantile-Based Approach for the Colombian Case
DOI: 10.5281/zenodo.15391765
title: data Asymmetric Impacts of the Energy Market on Stock Indexes in Emerging Economies: A Quantile-Based Approach for the Colombian Case
DOI: 10.15468/dl.fzysr4
title: Occurrence Download

description: A dataset containing 61584748 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is one of (Mexico, United States of America, Canada, Brazil, Venezuela (Bolivarian Republic of), Jamaica, Bahamas)",
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 61584748 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026975-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6tf74b
title: Occurrence Download

description: A dataset containing 110 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gastrotheca ochoai Duellman & Fritts, 1972"
 ]
}

 The dataset includes 110 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026979-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tt5rjm
title: Occurrence Download

description: A dataset containing 258 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "GadmGid is USA.5_1",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Carex tumulicola Mack."
 ]
}

 The dataset includes 258 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026980-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j6ga9e
title: Occurrence Download

description: A dataset containing 109 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Monodelphis americana (Müller, 1776)"
 ]
}

 The dataset includes 109 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026982-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11554820
title: modelforge curated dataset: QM9

description: Curated QM9 Dataset:

Full dataset, version full_dataset_v0:

This provides a curated hdf5 file for  the QM9 dataset to be used for testing purposes, designed to be compatible with modelforge, an infrastructure to implement and train NNPs.

When applicable, the units of properties are provided in the datafile,  encoded as strings compatible with the openff-units package.  For more information about the structure of the data file, please see the following:



https://github.com/choderalab/modelforge/wiki/Dataset-and-curation#curation-module


This curated dataset was generated using the modelforge software at commit c5c7153:



Link to the source code at this commit: https://github.com/choderalab/modelforge/tree/c5c7153e06172fe8e6f25015250ecb5db05655cc

Link to the script file used to generate the dataset: https://github.com/choderalab/modelforge/blob/c5c7153e06172fe8e6f25015250ecb5db05655cc/modelforge/curation/scripts/curate_qm9.py 


 

Original Source:

The QM9 dataset includes 133,885 organic molecules with up to nine total heavy atoms (C,O,N,or F; excluding H) original published by Ramakrishnan, et al. Properties in the QM9 dataset were calculated at the B3LYP/6-31G(2df,p) level of quantum chemistry.

Citations:

Original publication:



Ramakrishnan, R., Dral, P., Rupp, M. et al."Quantum chemistry structures and properties of 134 kilo molecules." Sci Data 1, 140022 (2014). https://doi.org/10.1038/sdata.2014.22


Source dataset, released with CCO 1.0 Universal license:



Ramakrishnan, Raghunathan; Dral, Pavlo; Rupp, Matthias; Anatole von Lilienfeld, O. (2014). Quantum chemistry structures and properties of 134 kilo molecules. figshare. Collection. https://doi.org/10.6084/m9.figshare.c.978904.v5
DOI: 10.5281/zenodo.11584283
title: modelforge curated dataset: QM9

description: Curated QM9 Dataset:

1000 conformer test set, version nc_1000_v0:

This provides a curated hdf5 file for a subset of the QM9 dataset to be used for testing purposes, designed to be compatible with modelforge, an infrastructure to implement and train NNPs.  This test dataset contains 1000 conformers, 1 for each unique molecule.

When applicable, the units of properties are provided in the datafile,  encoded as strings compatible with the openff-units package.  For more information about the structure of the data file, please see the following:



https://github.com/choderalab/modelforge/wiki/Dataset-and-curation#curation-module


This curated dataset was generated using the modelforge software at commit c5c7153:



Link to the source code at this commit: https://github.com/choderalab/modelforge/tree/c5c7153e06172fe8e6f25015250ecb5db05655cc

Link to the script file used to generate the dataset: https://github.com/choderalab/modelforge/blob/c5c7153e06172fe8e6f25015250ecb5db05655cc/modelforge/curation/scripts/curate_qm9.py 


 

Original Source:

The QM9 dataset includes 133,885 organic molecules with up to nine total heavy atoms (C,O,N,or F; excluding H) original published by Ramakrishnan, et al. Properties in the QM9 dataset were calculated at the B3LYP/6-31G(2df,p) level of quantum chemistry.

Citations:

Original publication:



Ramakrishnan, R., Dral, P., Rupp, M. et al."Quantum chemistry structures and properties of 134 kilo molecules." Sci Data 1, 140022 (2014). https://doi.org/10.1038/sdata.2014.22


Source dataset, released with CCO 1.0 Universal license:



Ramakrishnan, Raghunathan; Dral, Pavlo; Rupp, Matthias; Anatole von Lilienfeld, O. (2014). Quantum chemistry structures and properties of 134 kilo molecules. figshare. Collection. https://doi.org/10.6084/m9.figshare.c.978904.v5
DOI: 10.5281/zenodo.15390593
title: modelforge curated dataset: QM9

description: Modelforge Curated QM9 Dataset:- 1000 conformer test set- Version: nc_1000_v1.1:

This provides a curated hdf5 file for a subset of the QM9 dataset to be used for testing purposes, designed to be compatible with modelforge, an infrastructure to implement and train NNPs.  This test dataset contains 1000 configurations, 1 for each unique system.

When applicable, the units of properties are provided in the datafile,  encoded as strings compatible with the openff-units package.  For more information about the structure of the data file, please see the following:



https://github.com/choderalab/modelforge/wiki/Dataset-and-curation#curation-module


Properties Included:     



atomic_numbers 

positions      



 "per_atom"

"nanometer"



partial_charges



"per_atom"

"elementary_charge"



polarizability 



"per_system"

"nanometer ** 3"



dipole_moment_per_system       



"per_system"

"elementary_charge * nanometer"



dipole_moment_scalar_per_system



"per_system"

"elementary_charge * nanometer"



energy_of_homo 



"per_system"

"kilojoule_per_mole"



lumo-homo_gap  



"per_system"

"kilojoule_per_mole"



zero_point_vibrational_energy  



"per_system"

"kilojoule_per_mole"



internal_energy_at_298.15K     



"per_system"

"kilojoule_per_mole"



internal_energy_at_0K  



"per_system"

"kilojoule_per_mole"



enthalpy_at_298.15K    



"per_system"

"kilojoule_per_mole"



free_energy_at_298.15K 



"per_system"

"kilojoule_per_mole"



heat_capacity_at_298.15K       



"per_system"

"kilojoule_per_mole / kelvin"



rotational_constants   



"per_system"

"gigahertz"



harmonic_vibrational_frequencies       



"per_system"

"1 / centimeter"



electronic_spatial_extent      



"per_system"

"nanometer ** 2"



smiles_gdb-17  



 "meta_data"

"meta_data"



inchi_corina    



"meta_data"



inchi_b3lyp    



"meta_data"



idx    



"meta_data"



tag    



"meta_data"




Original Source:

The QM9 dataset includes 133,885 organic molecules with up to nine total heavy atoms (C,O,N,or F; excluding H) original published by Ramakrishnan, et al. Properties in the QM9 dataset were calculated at the B3LYP/6-31G(2df,p) level of quantum chemistry.

Citations:

Original publication:



Ramakrishnan, R., Dral, P., Rupp, M. et al."Quantum chemistry structures and properties of 134 kilo molecules." Sci Data 1, 140022 (2014). https://doi.org/10.1038/sdata.2014.22


Source dataset, released with CCO 1.0 Universal license:



Ramakrishnan, Raghunathan; Dral, Pavlo; Rupp, Matthias; Anatole von Lilienfeld, O. (2014). Quantum chemistry structures and properties of 134 kilo molecules. figshare. Collection. https://doi.org/10.6084/m9.figshare.c.978904.v5