cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.11397016
title: Pose Selector Workflow - Docking Poses, Absolute Binding Free Energy Estimates and Structure Input Files for Machine Learning

description: The Pose Selector (PS) workflow calculates absolute binding free energies (ABFEs) for binding poses of protein-ligand complexes. First, it converts the binding poses (both docking poses as well as experimentally observed ligand binding poses), which are provided as a combination of protein PDB file and ligand MOL2 file, into input files for molecular dynamics (MD) simulations with GROMACS after they have passed extensive quality checks and repair steps. Next, the PS workflow post-processes and analyses the last frame of the resulting eight 100 ps trajectories per binding pose with the Generalised Born model of implicit solvation as implemented in gmx_MMPBSA to obtain the ABFE estimates. The workflow was designed for soluble proteins without post-translational modifications, co-factors and non-standard amino acids, and it has limited support for coordinated ions.

For the dataset published here, the PS workflow was run on docking poses generated for the PDBbind 2020 dataset (http://www.pdbbind.org.cn/index.php), shared in dockingPosesPDBBind2020.tar.gz. This entry and its partner entry 10.5281/zenodo.11397486 also share the intial coordinates used in the MD simulations of >800,000 docking poses of 4022 protein-ligand complexes (structureFiles_dockingPoses1.tar.gz in this entry and structureFiles_dockingPoses2.tar.gz in 10.5281/zenodo.11397486) and of the experimental ligand binding pose of 4549 complexes (structureFiles_experimentalStructures.tar.gz) as well as the corresponding ABFE estimates (absoluteBindingFreeEnergyEstimates.tar.gz). The MD simulations were run on the LUMI and MeluXina supercomputers while the implicit-solvent calculations were carried out on Galileo (Cineca).

The README file describes the structure of the shared data in more detail and points out how to reproduce the MD trajectories and the subsequent implicit-solvent calculations yielding the free-energy estimates as well as how to use the data provided in this entry to train a machine-learning model predicting the ABFE of binding poses of protein-ligand complexes. The workflow scripts can be downloaded from GitHub (https://github.com/LigateProject/Pose-Selector-workflow). The MD simulations were run with GROMACS 2023.2 (https://manual.gromacs.org/2023.2/index.html), and the implicit-solvent calculations were carried out with gmx_MMPBSA 1.6.1 (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/v1.6.1/).
DOI: 10.5281/zenodo.11397017
title: Pose Selector Workflow - Docking Poses, Absolute Binding Free Energy Estimates and Structure Input Files for Machine Learning

description: The Pose Selector (PS) workflow calculates absolute binding free energies (ABFEs) for binding poses of protein-ligand complexes. First, it converts the binding poses (both docking poses as well as experimentally observed ligand binding poses), which are provided as a combination of protein PDB file and ligand MOL2 file, into input files for molecular dynamics (MD) simulations with GROMACS after they have passed extensive quality checks and repair steps. Next, the PS workflow post-processes and analyses the last frame of the resulting eight 100 ps trajectories per binding pose with the Generalised Born model of implicit solvation as implemented in gmx_MMPBSA to obtain the ABFE estimates. The workflow was designed for soluble proteins without post-translational modifications, co-factors and non-standard amino acids, and it has limited support for coordinated ions.

For the dataset published here, the PS workflow was run on docking poses generated for the PDBbind 2020 dataset (http://www.pdbbind.org.cn/index.php), shared in dockingPosesPDBBind2020.tar.gz. This entry and its partner entry 10.5281/zenodo.11397486 also share the intial coordinates used in the MD simulations of >800,000 docking poses of 4022 protein-ligand complexes (structureFiles_dockingPoses1.tar.gz in this entry and structureFiles_dockingPoses2.tar.gz in 10.5281/zenodo.11397486) and of the experimental ligand binding pose of 4549 complexes (structureFiles_experimentalStructures.tar.gz) as well as the corresponding ABFE estimates (absoluteBindingFreeEnergyEstimates.tar.gz). The MD simulations were run on the LUMI and MeluXina supercomputers while the implicit-solvent calculations were carried out on Galileo (Cineca).

The README file describes the structure of the shared data in more detail and points out how to reproduce the MD trajectories and the subsequent implicit-solvent calculations yielding the free-energy estimates as well as how to use the data provided in this entry to train a machine-learning model predicting the ABFE of binding poses of protein-ligand complexes. The workflow scripts can be downloaded from GitHub (https://github.com/LigateProject/Pose-Selector-workflow). The MD simulations were run with GROMACS 2023.2 (https://manual.gromacs.org/2023.2/index.html), and the implicit-solvent calculations were carried out with gmx_MMPBSA 1.6.1 (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/v1.6.1/).
DOI: 10.15468/dl.2bodyh
title: Occurrence Download

description: A dataset containing 37 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-76.46484 -41.90625,-65.21484 -41.90625,-65.21484 -23.625,-76.46484 -23.625,-76.46484 -41.90625))",
 "TaxonKey is Montiopsis sericea (Hook. & Arn.) D.I.Ford"
 ]
}

 The dataset includes 37 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030038-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/inscriptifact-ouc111316695
title: Leather Transaction

description: [Text Description:] Cuneiform Tablet, Leather Transaction ❧ [Medium:] Clay ❧ [Script Note:] Cuneiform, Non-Alphabetic ❧ [Physical Object Description:] Clay tablet with cuneiform script
DOI: 10.15468/dl.myu755
title: Occurrence Download

description: A dataset containing 59 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Geometry POLYGON((-48.47168 -29.15216,-46.27441 -26.43123,-47.06543 -23.64452,-48.03223 -21.37124,-53.39355 -21.28937,-55.23926 -23.32208,-56.29395 -25.48295,-55.85449 -27.83908,-53.39355 -30.90222,-50.22949 -31.27855,-48.47168 -29.15216))",
 "Geometry POLYGON((-46.42822 -22.87744,-45.19775 -24.20689,-42.29736 -23.07973,-43.04443 -21.77991,-43.92334 -20.59165,-45.68115 -20.96144,-46.42822 -22.87744))"
 ]
 },
 "HasCoordinate is true",
 "TaxonKey is Solanum pinetorum (L.B.Sm. & Downs) Bohs",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 59 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051261-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/inscriptifact-ouc111359323
title: Persepolis Fortification Elamite Tablet 1290.102, Fort 1290.102

description: [Text Description:] Administrative text ❧ [Text or Publication Number Note:] Fort 1290.102 ❧ [Excavation Description:] Found during Oriental Institute's excavations in Spring, 1933, near the northeastern corner of the stone platform of Persepolis, in two small rooms of a bastion in the fortification wall ❧ [Medium:] Clay ❧ [Script Note:] Non-Alphabetic Cuneiform ❧ [Physical Object Description:] Clay tablet with cuneiform text. Seal impression on upper edge. ❧ [Physical Object Note:] Left edge broken off, part of bottom edge. Top left of reverse broken off. ❧ [Physical Object Note:] Two tablets joined together: Fort 2177.101 is right half; Fort 1290.102 is left half.
DOI: 10.25549/inscriptifact-ouc111359461
title: Persepolis Fortification Elamite Tablet 1290.102, Fort 1290.102

description: [Text Description:] Administrative text ❧ [Text or Publication Number Note:] Fort 1290.102 ❧ [Excavation Description:] Found during Oriental Institute's excavations in Spring, 1933, near the northeastern corner of the stone platform of Persepolis, in two small rooms of a bastion in the fortification wall ❧ [Medium:] Clay ❧ [Script Note:] Non-Alphabetic Cuneiform ❧ [Physical Object Description:] Clay tablet with cuneiform text. Seal impression on upper edge. ❧ [Physical Object Note:] Left edge broken off, part of bottom edge. Top left of reverse broken off. ❧ [Physical Object Note:] Two tablets joined together: Fort 2177.101 is right half; Fort 1290.102 is left half.
DOI: 10.15468/dl.fhu3xx
title: Occurrence Download

description: A dataset listing the 14 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-92.27637 18.02209,-91.52985 17.81551,-91.47217 18.45356,-91.65454 18.44991,-92.01929 18.60825,-92.27637 18.02209))",
 "TaxonKey is Amphibia",
 "HasGeospatialIssue is false"
 ]
}

 The dataset's 14 records were derived from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059092-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vqae2d
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Allium sphaerocephalon var. stipitatum Radić, 1989"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0063151-240506114902167/datasets/export for details.
DOI: 10.25549/inscriptifact-ouc111294232
title: Nehemiah 2:13-16, DSS F.201

description: [Text Description:] DSS F.201; inspecting the walls of Jerusalem ❧ [Text or Publication Number Note:] MOTB.SCR.003175; DSS F.Neh2; DSS F.201 ❧ [Medium:] Parchment ❧ [Script Note:] Jewish ❧ [Physical Object Description:] Substrate is dark brown, surface worn in some places, revealing lighter areas. ❧ [Physical Object Note:] Two pieces vertically joined to measure a combined 2.1 x 3.4cm. ❧ [Physical Object Note:] Four lines of text in the middle of a column. Letters visible to naked eye. No visible ruling lines. ❧
DOI: 10.15468/dl.a7ehtr
title: Occurrence Download

description: A dataset containing 27 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cryptotis colombiana Woodman & Timm, 1993"
 ]
}

 The dataset includes 27 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059096-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/inscriptifact-ouc111296228
title: El-Qom Tomb Inscription, HITBP Qom 3, Khirbet el-Qom Tomb Inscription, Uriah Tomb Inscription

description: [Text Description:] Uriah tomb inscription with upside-down hand ❧ [Text or Publication Number Note:] HITBP Qom 3, IAA 1972-169 ❧ [Excavation Description:] Cut from Tomb II, east wall of central room, between entrances to Chambers 1 & 2 by grave robbers ❧ [Medium:] Stone ❧ [Script Note:] Hebrew ❧ [Physical Object Description:] Tomb inscription cut from Tomb II; extraneous scratches and cracks; vertical lines and faults ❧ [Physical Object Note:] Vertical lines may be tool marks; deep upside-down imprint of right hand ❧ [Physical Object Note:] 6 lines; letters may have been traced over; bottom of inscription broken off ❧
DOI: 10.25549/inscriptifact-ouc111299000
title: Sinai Syriac 30: Lives of Holy Women, Sinai Syriac 30: Lives of Holy Women, Syrus Sinaiticus

description: [Text Description:] Stories and meditations on holy women/saints, including those who were martyrs, and those in the Bible and Deuterocanonical literature. ❧ [Text or Publication Number Note:] Sinai Syriac 30: Lives of Holy Women ❧ [Medium:] Parchment ❧ [Script Note:] Syriac: Estrangela ❧ [Physical Object Description:] Palimpsest, with overtext written in Syriac, undertext in Syriac or Greek. Ink on overtext is black, ink on undertext has oxidized to faded brown. ❧ [Physical Object Note:] Many of the pages show some water damage. ❧ [Physical Object Note:] Back cover is still extant, shows evidence of roughly stitched repair. ❧
DOI: 10.15468/dl.77fgxx
title: Occurrence Download

description: A dataset containing 464 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Mexico",
 "TaxonKey is Funaria hygrometrica Hedw."
 ]
}

 The dataset includes 464 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027530-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/inscriptifact-ouc111296233
title: El-Qom Tomb Inscription, HITBP Qom 3, Khirbet el-Qom Tomb Inscription, Uriah Tomb Inscription

description: [Text Description:] Uriah tomb inscription with upside-down hand ❧ [Text or Publication Number Note:] HITBP Qom 3, IAA 1972-169 ❧ [Excavation Description:] Cut from Tomb II, east wall of central room, between entrances to Chambers 1 & 2 by grave robbers ❧ [Medium:] Stone ❧ [Script Note:] Hebrew ❧ [Physical Object Description:] Tomb inscription cut from Tomb II; extraneous scratches and cracks; vertical lines and faults ❧ [Physical Object Note:] Vertical lines may be tool marks; deep upside-down imprint of right hand ❧ [Physical Object Note:] 6 lines; letters may have been traced over; bottom of inscription broken off ❧
DOI: 10.25549/inscriptifact-ouc111296237
title: El-Qom Tomb Inscription, HITBP Qom 3, Khirbet el-Qom Tomb Inscription, Uriah Tomb Inscription

description: [Text Description:] Uriah tomb inscription with upside-down hand ❧ [Text or Publication Number Note:] HITBP Qom 3, IAA 1972-169 ❧ [Excavation Description:] Cut from Tomb II, east wall of central room, between entrances to Chambers 1 & 2 by grave robbers ❧ [Medium:] Stone ❧ [Script Note:] Hebrew ❧ [Physical Object Description:] Tomb inscription cut from Tomb II; extraneous scratches and cracks; vertical lines and faults ❧ [Physical Object Note:] Vertical lines may be tool marks; deep upside-down imprint of right hand ❧ [Physical Object Note:] 6 lines; letters may have been traced over; bottom of inscription broken off ❧
DOI: 10.15468/dl.vgu7eb
title: Occurrence Download

description: A dataset containing 46 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Geometry POLYGON((-48.47168 -29.15216,-46.27441 -26.43123,-47.06543 -23.64452,-48.03223 -21.37124,-53.39355 -21.28937,-55.23926 -23.32208,-56.29395 -25.48295,-55.85449 -27.83908,-53.39355 -30.90222,-50.22949 -31.27855,-48.47168 -29.15216))",
 "Geometry POLYGON((-46.42822 -22.87744,-45.19775 -24.20689,-42.29736 -23.07973,-43.04443 -21.77991,-43.92334 -20.59165,-45.68115 -20.96144,-46.42822 -22.87744))"
 ]
 },
 "HasCoordinate is true",
 "TaxonKey is Solanum wacketii Witasek",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 46 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051280-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/inscriptifact-ouc111360771
title: Persepolis Fortification Elamite Tablet 2012.104, Fort 2012.104

description: [Text Description:] Administrative text ❧ [Text or Publication Number Note:] Fort 2012.104 ❧ [Excavation Description:] Found during Oriental Institute's excavations in Spring, 1933, near the northeastern corner of the stone platform of Persepolis, in two small rooms of a bastion in the fortification wall ❧ [Medium:] Clay ❧ [Script Note:] Non-Alphabetic Cuneiform ❧ [Physical Object Description:] Clay tablet with cuneiform text. Seal impression on upper edge. ❧ [Physical Object Note:] Several fragments joined together. Lower right of original tablet broken off. Cracks and abrasions on obverse, reverse. ❧ [Physical Object Note:] Top left quadrant is Fort 2009.102; bottom left is Fort 2012.102; top right is Fort 2012.104.
DOI: 10.25549/inscriptifact-ouc111317169
title: Cuneiform Tablet 93

description: [Text Description:] Cuneiform Tablet 93 ❧ [Medium:] Clay ❧ [Script Note:] Cuneiform, Non-Alphabetic ❧ [Physical Object Description:] Clay tablet with cuneiform script
DOI: 10.15468/dl.x5sdw4
title: Occurrence Download

description: A dataset containing 2793 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Spodoptera frugiperda J.E.Smith, 1797"
 ]
}

 The dataset includes 2793 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043030-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/inscriptifact-ouc111317007
title: Cuneiform Tablet 93

description: [Text Description:] Cuneiform Tablet 93 ❧ [Medium:] Clay ❧ [Script Note:] Cuneiform, Non-Alphabetic ❧ [Physical Object Description:] Clay tablet with cuneiform script
DOI: 10.25549/inscriptifact-ouc111296260
title: El-Qom Tomb Inscription, HITBP Qom 3, Khirbet el-Qom Tomb Inscription, Uriah Tomb Inscription

description: [Text Description:] Uriah tomb inscription with upside-down hand ❧ [Text or Publication Number Note:] HITBP Qom 3, IAA 1972-169 ❧ [Excavation Description:] Cut from Tomb II, east wall of central room, between entrances to Chambers 1 & 2 by grave robbers ❧ [Medium:] Stone ❧ [Script Note:] Hebrew ❧ [Physical Object Description:] Tomb inscription cut from Tomb II; extraneous scratches and cracks; vertical lines and faults ❧ [Physical Object Note:] Vertical lines may be tool marks; deep upside-down imprint of right hand ❧ [Physical Object Note:] 6 lines; letters may have been traced over; bottom of inscription broken off ❧
DOI: 10.25549/inscriptifact-ouc111296262
title: El-Qom Tomb Inscription, HITBP Qom 3, Khirbet el-Qom Tomb Inscription, Uriah Tomb Inscription

description: [Text Description:] Uriah tomb inscription with upside-down hand ❧ [Text or Publication Number Note:] HITBP Qom 3, IAA 1972-169 ❧ [Excavation Description:] Cut from Tomb II, east wall of central room, between entrances to Chambers 1 & 2 by grave robbers ❧ [Medium:] Stone ❧ [Script Note:] Hebrew ❧ [Physical Object Description:] Tomb inscription cut from Tomb II; extraneous scratches and cracks; vertical lines and faults ❧ [Physical Object Note:] Vertical lines may be tool marks; deep upside-down imprint of right hand ❧ [Physical Object Note:] 6 lines; letters may have been traced over; bottom of inscription broken off ❧
DOI: 10.15468/dl.9fxm24
title: Occurrence Download

description: A dataset containing 4583 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 "Geometry POLYGON((-4.08691 36.55201,-2.31812 36.63933,-1.97754 37.56896,-4.08691 37.56896,-4.08691 36.55201))",
 "HasGeospatialIssue is false",
 "TaxonKey is Plantae",
 "Year 1000-1970"
 ]
}

 The dataset includes 4583 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029711-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/inscriptifact-ouc111296206
title: El-Qom Tomb Inscription, HITBP Qom 3, Khirbet el-Qom Tomb Inscription, Uriah Tomb Inscription

description: [Text Description:] Uriah tomb inscription with upside-down hand ❧ [Text or Publication Number Note:] HITBP Qom 3, IAA 1972-169 ❧ [Excavation Description:] Cut from Tomb II, east wall of central room, between entrances to Chambers 1 & 2 by grave robbers ❧ [Medium:] Stone ❧ [Script Note:] Hebrew ❧ [Physical Object Description:] Tomb inscription cut from Tomb II; extraneous scratches and cracks; vertical lines and faults ❧ [Physical Object Note:] Vertical lines may be tool marks; deep upside-down imprint of right hand ❧ [Physical Object Note:] 6 lines; letters may have been traced over; bottom of inscription broken off ❧
DOI: 10.25549/inscriptifact-ouc111293067
title: A Fragment of Instruction, DSS F.202

description: [Text Description:] DSS F.202; Parts of 2 lines resembling 4Q415 ❧ [Text or Publication Number Note:] MOTB.SCR.000123; DSS F.Instruction; DSS F.202 ❧ [Medium:] Parchment ❧ [Script Note:] Jewish ❧ [Physical Object Description:] Leather is dark brown. Most of surface is abraded, revealing lighter brown. ❧ [Physical Object Note:] Fragment measures 4.65 x 1.56cm. ❧ [Physical Object Note:] Beginnings of two lines preserved along a right margin. Writing difficult to see in natural light. May be traces of vertical ruling. ❧
DOI: 10.15468/dl.exu42e
title: Occurrence Download

description: A dataset listing the 684 species recorded in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Observation",
 "BasisOfRecord is Machine Observation",
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Material sample",
 "BasisOfRecord is Literature Occurrence",
 "BasisOfRecord is Unknown evidence"
 ]
 },
 "Country is Saint Kitts and Nevis",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset's 684 records were derived from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065096-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/inscriptifact-ouc111293113
title: A Fragment of Instruction, DSS F.202

description: [Text Description:] DSS F.202; Parts of 2 lines resembling 4Q415 ❧ [Text or Publication Number Note:] MOTB.SCR.000123; DSS F.Instruction; DSS F.202 ❧ [Medium:] Parchment ❧ [Script Note:] Jewish ❧ [Physical Object Description:] Leather is dark brown. Most of surface is abraded, revealing lighter brown. ❧ [Physical Object Note:] Fragment measures 4.65 x 1.56cm. ❧ [Physical Object Note:] Beginnings of two lines preserved along a right margin. Writing difficult to see in natural light. May be traces of vertical ruling. ❧
DOI: 10.15468/dl.cwcbhg
title: Occurrence Download

description: A dataset containing 283082 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ulmus minor Mill."
 ]
}

 The dataset includes 283082 records from 2363 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0063139-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15483/2997699
title: Baseline vs. DER Scenario

description: Projections and associated uncertainty estimates are generated for a variety of user-selectable EV charging sessions, electricity tariffs, subsidy levels, revenue schemes, charging station configurations, and on-site solar and/or storage options. The outputs are presented in CHIP's web portal browser in the form of easily interpretable graphics (interactive graphs and bar charts) that facilitate convenient comparison among different scenarios to aid decision-making. The user should bring assumptions for modeling on simulation planning horizon, number of EV charging sessions per year, electricity costs (energy and demand charge rates; flat versus time-of-use rate), site capital costs (equipment for EV chargers and transformer), solar PV, and battery energy storage (kW).