cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccsmm11
title: CCDC 733833: Experimental Crystal Structure Determination

description: Related Article: J.J.Allen, C.E.Hamilton, A.R.Barron|2010|Dalton Trans.|39|11451|doi:10.1039/c0dt00608d
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccsp7k7
title: CCDC 735399: Experimental Crystal Structure Determination

description: Related Article: J.J.Allen, C.E.Hamilton, A.R.Barron|2010|Dalton Trans.|39|11451|doi:10.1039/c0dt00608d
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccsv5vm
title: CCDC 740151: Experimental Crystal Structure Determination

description: Related Article: J.J.Allen, C.E.Hamilton, A.R.Barron|2010|Dalton Trans.|39|11451|doi:10.1039/c0dt00608d
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccsyn9n
title: CCDC 743482: Experimental Crystal Structure Determination

description: Related Article: J.J.Allen, C.E.Hamilton, A.R.Barron|2010|Dalton Trans.|39|11451|doi:10.1039/c0dt00608d
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccv4ztr
title: CCDC 779365: Experimental Crystal Structure Determination

description: Related Article: C.N.Kato, Y.Katayama, M.Nagami, M.Kato, M.Yamasaki|2010|Dalton Trans.|39|11469|doi:10.1039/c0dt00722f
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccv8zmp
title: CCDC 783203: Experimental Crystal Structure Determination

description: Related Article: J.C.Knight, R.Prabaharan, B.D.Ward, A.J.Amoroso, P.G.Edwards, B.M.Kariuki|2010|Dalton Trans.|39|10031|doi:10.1039/c0dt01205j
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cctncng
title: CCDC 764356: Experimental Crystal Structure Determination

description: Related Article: Xiang Zhu, Cheng He, Dapeng Dong, Yang Liu, Chunying Duan|2010|Dalton Trans.|39|10051|doi:10.1039/c002278k
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cctrhrs
title: CCDC 767366: Experimental Crystal Structure Determination

description: Related Article: M.Kumar, V.Bhalla, A.Dhir, J.N.Babu|2010|Dalton Trans.|39|10116|doi:10.1039/c0dt00804d
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cctqh22
title: CCDC 766384: Experimental Crystal Structure Determination

description: Related Article: K.Srivastava, T.Chakraborty, H.B.Singh, U.P.Singh, R.J.Butcher|2010|Dalton Trans.|39|10137|doi:10.1039/c0dt00509f
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccvbrb7
title: CCDC 784899: Experimental Crystal Structure Determination

description: Related Article: Xiuli Wan, Jinxia Zhang, Guocheng Liu, Hongyan Lin|2011|J.Solid State Chem.|184|280|doi:10.1016/j.jssc.2010.11.016
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccvbrc8
title: CCDC 784900: Experimental Crystal Structure Determination

description: Related Article: Xiuli Wan, Jinxia Zhang, Guocheng Liu, Hongyan Lin|2011|J.Solid State Chem.|184|280|doi:10.1016/j.jssc.2010.11.016
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccvbrd9
title: CCDC 784901: Experimental Crystal Structure Determination

description: Related Article: Xiuli Wan, Jinxia Zhang, Guocheng Liu, Hongyan Lin|2011|J.Solid State Chem.|184|280|doi:10.1016/j.jssc.2010.11.016
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccvbrfb
title: CCDC 784902: Experimental Crystal Structure Determination

description: Related Article: Xiuli Wan, Jinxia Zhang, Guocheng Liu, Hongyan Lin|2011|J.Solid State Chem.|184|280|doi:10.1016/j.jssc.2010.11.016
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccvbrgc
title: CCDC 784903: Experimental Crystal Structure Determination

description: Related Article: Xiuli Wan, Jinxia Zhang, Guocheng Liu, Hongyan Lin|2011|J.Solid State Chem.|184|280|doi:10.1016/j.jssc.2010.11.016
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccvbrhd
title: CCDC 784904: Experimental Crystal Structure Determination

description: Related Article: Xiuli Wan, Jinxia Zhang, Guocheng Liu, Hongyan Lin|2011|J.Solid State Chem.|184|280|doi:10.1016/j.jssc.2010.11.016
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cctrxjz
title: CCDC 767762: Experimental Crystal Structure Determination

description: Related Article: F.Hussain, S.Sandriesser, M.Splendrich, G.R.Patzke|2011|J.Solid State Chem.|184|214|doi:10.1016/j.jssc.2010.11.005
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccvbrjf
title: CCDC 784905: Experimental Crystal Structure Determination

description: Related Article: Xiuli Wan, Jinxia Zhang, Guocheng Liu, Hongyan Lin|2011|J.Solid State Chem.|184|280|doi:10.1016/j.jssc.2010.11.016
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cctrxk0
title: CCDC 767763: Experimental Crystal Structure Determination

description: Related Article: F.Hussain, S.Sandriesser, M.Splendrich, G.R.Patzke|2011|J.Solid State Chem.|184|214|doi:10.1016/j.jssc.2010.11.005
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cctrxl1
title: CCDC 767764: Experimental Crystal Structure Determination

description: Related Article: F.Hussain, S.Sandriesser, M.Splendrich, G.R.Patzke|2011|J.Solid State Chem.|184|214|doi:10.1016/j.jssc.2010.11.005
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cctrxm2
title: CCDC 767765: Experimental Crystal Structure Determination

description: Related Article: F.Hussain, S.Sandriesser, M.Splendrich, G.R.Patzke|2011|J.Solid State Chem.|184|214|doi:10.1016/j.jssc.2010.11.005
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cctrxn3
title: CCDC 767766: Experimental Crystal Structure Determination

description: Related Article: F.Hussain, S.Sandriesser, M.Splendrich, G.R.Patzke|2011|J.Solid State Chem.|184|214|doi:10.1016/j.jssc.2010.11.005
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.15468/dl.tmc6fe
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Castanopsis wenchangensis)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045378-251009101135966/datasets/export for details.
DOI: 10.15468/dl.6qx6xr
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Arachnida)",
 "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((22.5 7.5,30 7.5,30 15,22.5 15,22.5 7.5))"
 ]
}

 The dataset includes 9 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045379-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jtu56x
title: Occurrence Download

description: A dataset containing 978 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Australia",
 "TaxonKey is Oedura castelnaui"
 ]
}

 The dataset includes 978 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045380-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ke7qem
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Sphenodontia, Crocodylia, Squamata, Testudines)",
 "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((127.5 82.5,135 82.5,135 90,127.5 90,127.5 82.5))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045381-251009101135966/datasets/export for details.
DOI: 10.5281/zenodo.17402609
title: OpenFF 2.3.0rc1 Relative Binding Free Energy Benchmarks

description: Overview

Relative binding free energy benchmarks of the openff-2.3.0rc1 release using the JACS set from (https://github.com/OpenFreeEnergy/IndustryBenchmarks2024).

Contents

Benchmark variants

The following benchmark variants were run:  * `openff-2.3.0rc1_elf10`: simulations using OpenFF 2.3.0rc1 and AM1BCCELF10 charges using the OpenEye Toolkit.  * `openff-2.3.0rc1_nagl`: simulations using OpenFF 2.3.0rc1 and AshGC v0.1rc3 charges

RBFE data

The `data` folder contains all the ddG data for each transformation in each set. These are stored as TSV files within subdirectories for each system in the JACS set.

Per system data files

These are stored as TSV files within subdirectories for each system in the JACS set.Reference CSV data (labelled as `{system}_ref.csv`), taken from the Ross et al. 2023 dataset (https://github.com/schrodinger/public_binding_free_energy_benchmark)can alsos be found.

Aggregate dG and ddG files

CSV files with all the dG and ddG values for all datasets can be found in `data`.

Simulation details

* All simulations were carried out using the RelativeHybridTopology protocol in OpenFE v1.4.* Mappings were created using Kartograf, these are the same as those used in the OpenFE industry benchmarks.* Transformation edges were created using Lomap, these are the same as those used in the OpenFE industry benchmarks.* Simulations used openfe default settings, except the following:  * Dodecahedron solvent box with 1 nm padding in complex and 1.5 nm padding in solvent  * 2.5 ps HREX exchange rate  * 0.9 nm short range interaction cutoff
DOI: 10.15468/dl.yrvuu4
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Arachnida)",
 "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((15 7.5,22.5 7.5,22.5 15,15 15,15 7.5))"
 ]
}

 The dataset includes 15 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045382-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jfyns9
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Sphenodontia, Crocodylia, Squamata, Testudines)",
 "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((-120 -90,-112.5 -90,-112.5 -82.5,-120 -82.5,-120 -90))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045384-251009101135966/datasets/export for details.
DOI: 10.15468/dl.dvu4h7
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Sphenodontia, Crocodylia, Squamata, Testudines)",
 "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((135 82.5,142.5 82.5,142.5 90,135 90,135 82.5))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045385-251009101135966/datasets/export for details.
DOI: 10.15468/dl.95gamf
title: Occurrence Download

description: A dataset containing 40487 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Arachnida)",
 "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((-105 22.5,-97.5 22.5,-97.5 30,-105 30,-105 22.5))"
 ]
}

 The dataset includes 40487 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045383-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2zhxar
title: Occurrence Download

description: A dataset containing 227 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "TaxonKey is Phymatidium delicatulum"
 ]
}

 The dataset includes 227 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045386-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3gsrq7
title: Occurrence Download

description: A dataset containing 67 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Australocosmica"
 ]
}

 The dataset includes 67 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045387-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r4m6tg
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "TaxonKey is Ouleus panna"
 ]
}

 The dataset includes 7 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045388-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/13448337
title: Dataset jadwal event lariku.info
DOI: 10.6084/m9.figshare.30403228
title: Chromosome-level genome assembly of Lonchoptera multiseta

description: Lonchoptera multisetais a newly described species of pointed-wing fly (Diptera: Lonchopteridae) endemic to the Loess Plateau subregion of China, characterized by its unique male genital morphology with multiple elongated setae. This genome provides a valuable resource for future studies on the evolution, ecology, and population genetics of Lonchopteridae and other related dipteran groups.
DOI: 10.6084/m9.figshare.30403228.v1
title: Chromosome-level genome assembly of Lonchoptera multiseta

description: Lonchoptera multisetais a newly described species of pointed-wing fly (Diptera: Lonchopteridae) endemic to the Loess Plateau subregion of China, characterized by its unique male genital morphology with multiple elongated setae. This genome provides a valuable resource for future studies on the evolution, ecology, and population genetics of Lonchopteridae and other related dipteran groups.
DOI: 10.5281/zenodo.17402622
title: OpenFF 2.2.1 Relative Binding Free Energy Benchmarks

description: OpenFF 2.2.1 Relative Binding Free Energy Benchmarks

Overview

Relative binding free energy benchmarks of the openff-2.2.1 release using the JACS set from (https://github.com/OpenFreeEnergy/IndustryBenchmarks2024).

Contents

Benchmark variants

The following benchmark variants were run:  * `openff-2.2.1_elf10`: simulations using OpenFF 2.2.1 and AM1BCCELF10 charges using the OpenEye Toolkit.  * `openff-2.2.1_nagl`: simulations using OpenFF 2.2.1 and AshGC v0.1rc3 charges  * `openff-2.2.1_am1bcc`: simulations using OpenFF 2.2.1 and AM1BCC charges calculated using ambertools. Please note that these charges were not assigned to the input conformer, but rather a conformer that was generated at charge assignment time via RDKit through the OpenFF toolkit.

RBFE data

The `data` folder contains all the ddG data for each transformation in each set. These are stored as TSV files within subdirectories for each system in the JACS set.

Per system data files

These are stored as TSV files within subdirectories for each system in the JACS set.Reference CSV data (labelled as `{system}_ref.csv`), taken from the Ross et al. 2023 dataset (https://github.com/schrodinger/public_binding_free_energy_benchmark)can alsos be found.

Aggregate dG and ddG files

CSV files with all the dG and ddG values for all datasets can be found in `data`.

Simulation details

* All simulations were carried out using the RelativeHybridTopology protocol in OpenFE v1.4.* Mappings were created using Kartograf, these are the same as those used in the OpenFE industry benchmarks.* Transformation edges were created using Lomap, these are the same as those used in the OpenFE industry benchmarks.* Simulations used openfe default settings, except the following:  * Dodecahedron solvent box with 1 nm padding in complex and 1.5 nm padding in solvent  * 2.5 ps HREX exchange rate  * 0.9 nm short range interaction cutoff