cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7575846
title: Supplements for "Solvent Accessibility Promotes Rotamer Errors During Protein Modelling with Major Side-Chain Prediction Programs"

description: Supplements for "Solvent Accessibility Promotes Rotamer Errors During Protein Modelling with Major Side-Chain Prediction Programs"

This supplement includes the following files:



Main_v02.R --- Script in R language to process files (in "PDBs.zip") and produce the dataset ("Dataset_v02.csv")

PDBs.zip --- PDB files include filtered structures processed by three programs

Dataset_v02.csv --- final filtered version of dataset produced in R language (by "Main_v02.R").   

Dataset key.txt --- key to column names in Dataset_v02.csv     


The article featuring this dataset is published in:

Journal:  Journal of Chemical Information and ModelingTitle: "Solvent Accessibility Promotes Rotamer Errors During Protein Modelling with Major Side-Chain Prediction Programs"Author(s): Hameduh, Tareq; Mokry, Michal ; Miller, Andrew  ; Heger, Zbynek; Haddad, Yazan

https://pubs.acs.org/doi/10.1021/acs.jcim.3c00134

        
description: This work was supported by Internal Grant Agency of Mendel University in Brno [AF-IGA2022-IP-081]; Czech Health Research Council [NU21J-08-00043]; Czech Science Foundation [22-14568S]; Czech Ministry of Education, Youth and Sports OPVVV Project FIT (Pharmacology, Immunotherapy, nanoToxicology) [CZ.02.1.01/0.0/0.0/15_003/0000495] awarded to ADM with financial support from the European Regional Development Fund.
DOI: 10.5281/zenodo.7575847
title: Supplements for "Solvent Accessibility Promotes Rotamer Errors During Protein Modelling with Major Side-Chain Prediction Programs"

description: <strong>Supplements for "Solvent Accessibility Promotes Rotamer Errors During Protein Modelling with Major Side-Chain Prediction Programs"</strong> This supplement includes the following files: Main.R --- Script in R language to process files (in "pdb.zip") and produce the datasets ("Datasets.zip") functions.zip --- supplementary functions to the R script (in "Main.R") pdb.zip --- PDB files include filtered structures processed by three programs Datasets.zip --- Three versions of dataset produced in R language (by "Main.R"). The first two versions may contain unfiltered structures The article featuring this dataset is submitted to: Journal: Journal of Chemical Information and Modeling<br> Manuscript ID: ci-2023-00134a<br> Title: "Solvent Accessibility Promotes Rotamer Errors During Protein Modelling with Major Side-Chain Prediction Programs"<br> Author(s): Hameduh, Tareq; Mokry, Michal ; Miller, Andrew ; Heger, Zbynek; Haddad, Yazan
description: This work was supported by Internal Grant Agency of Mendel University in Brno [AF-IGA2022-IP-081]; Czech Health Research Council [NU21J-08-00043]; Czech Science Foundation [22-14568S]; Czech Ministry of Education, Youth and Sports OPVVV Project FIT (Pharmacology, Immunotherapy, nanoToxicology) [CZ.02.1.01/0.0/0.0/15_003/0000495] awarded to ADM with financial support from the European Regional Development Fund.
DOI: 10.5281/zenodo.7934793
title: Supplements for "Solvent Accessibility Promotes Rotamer Errors During Protein Modelling with Major Side-Chain Prediction Programs"

description: Supplements for "Solvent Accessibility Promotes Rotamer Errors During Protein Modelling with Major Side-Chain Prediction Programs"

This supplement includes the following files:



Main_v02.R --- Script in R language to process files (in "PDBs.zip") and produce the dataset ("Dataset_v02.csv")

PDBs.zip --- PDB files include filtered structures processed by three programs

Dataset_v02.csv --- final filtered version of dataset produced in R language (by "Main_v02.R").   

Dataset key.txt --- key to column names in Dataset_v02.csv     


The article featuring this dataset is published in:

Journal:  Journal of Chemical Information and ModelingTitle: "Solvent Accessibility Promotes Rotamer Errors During Protein Modelling with Major Side-Chain Prediction Programs"Author(s): Hameduh, Tareq; Mokry, Michal ; Miller, Andrew  ; Heger, Zbynek; Haddad, Yazan

https://pubs.acs.org/doi/10.1021/acs.jcim.3c00134

        
description: This work was supported by Internal Grant Agency of Mendel University in Brno [AF-IGA2022-IP-081]; Czech Health Research Council [NU21J-08-00043]; Czech Science Foundation [22-14568S]; Czech Ministry of Education, Youth and Sports OPVVV Project FIT (Pharmacology, Immunotherapy, nanoToxicology) [CZ.02.1.01/0.0/0.0/15_003/0000495] awarded to ADM with financial support from the European Regional Development Fund.
DOI: 10.5518/823
title: Data associated with 'Aggregation Behaviour of E-SARA Asphaltene Fractions Studied by Small-angle Neutron Scattering'

description: Using the Extended-SARA method to fractionate asphaltenes based on their interfacial activity, the current study reports the first results on the estimated size and shape of interfacially active (IAA) and remaining (RA) asphaltene nanoaggregates. These fractions have been reported to exhibit distinctly different chemical architectures that influence the size of asphaltene clusters in good and poor solvents. However, little is known about the building blocks, commonly referred to as nanoaggregates, which form these clusters and how those subtle differences in chemical architecture impact aggregation of asphaltenes. The nanoaggregate size and shape of IAA and RA was measured using small-angle neutron scattering (SANS). The characteristic length and asymptotic power-law exponent of whole asphaltenes (WA) extracted from heavy crude oil and dispersed in deuterated toluene were 28.0 Å 0.2 Å and 2.860.01, respectively, showing negligible variations with changing asphaltene concentration, source of asphaltenes (bitumen and heavy crude oil), and solvent aromaticity. For RA fractions, which account for 98.5 wt% of WA, the characteristic length and power-law exponent of 28.8 Å and 2.86 were comparable to that of WA, but in contrast to 59.7 Å and 2.20 for IAA.  A ~100% increase in the characteristic length and reduced power-law exponent of the IAA fraction confirms that these two asphaltene sub-fractions form dissimilar nanoaggregate structures.
DOI: 10.5281/zenodo.12723700
title: DAF-MIT AIA Open Flight Data for Magnetic Navigation Research

description: This dataset was developed as part of the DAF-MIT Artificial Intelligence Accelerator to support research on airborne magnetic anomaly navigation (MagNav), an alternative to GPS. Flight data was collected during the summer of 2020 by Sander Geophysics Ltd. (SGL) near Ottawa, Ontario, Canada using a Cessna Grand Caravan equipped with a number of sensors.

Within the dataset is a nearly perfect signal of the Earth's magnetic field (minimal aircraft interference) from tail stinger (boom) measurements, as well as four noisy magnetic signals (varying degrees of aircraft interference) from in-aircraft measurements. These scalar measurements of the total field were generated from five optically pumped, split-beam cesium vapor magnetometers. Additionally, four fluxgate magnetometers were used for vector measurements of the total field. The dataset also contains supplemental sensor data from the inertial navigation system, GPS position data, voltages, currents, and more.

During the data collection flights, various events were purposely carried out to cause temporal magnetic field disturbances. This included control surface movements (e.g., flaps up/down), fuel pump on/off, radio use, and movement of magnetic materials within the cabin. The flight patterns and altitudes were also varied from flight to flight to provide a diverse dataset. Please see the provided datasheet for further high-level dataset information and the readmes for individual flight details.

As of release v3 this data includes both year 1 of the collection (Flights 1002-1007) and year 2 of the collection (Flights 2001-2017) which correspond to 2020 and 2021 respectively. The zip files that are now available include information about the various fields available in each collection with the flight specific readmes including flight plan information (survey line vs transit, etc).

This dataset supports the Signal Enhancement for Magnetic Navigation Challenge Problem: https://magnav.mit.edu
DOI: 10.5281/zenodo.4271803
title: DAF-MIT AIA Open Flight Data for Magnetic Navigation Research

description: This dataset was developed as part of the DAF-MIT Artificial Intelligence Accelerator to support research on airborne magnetic anomaly navigation (MagNav), an alternative to GPS. Flight data was collected during the summer of 2020 by Sander Geophysics Ltd. (SGL) near Ottawa, Ontario, Canada using a Cessna Grand Caravan equipped with a number of sensors.

Within the dataset is a nearly perfect signal of the Earth's magnetic field (minimal aircraft interference) from tail stinger (boom) measurements, as well as four noisy magnetic signals (varying degrees of aircraft interference) from in-aircraft measurements. These scalar measurements of the total field were generated from five optically pumped, split-beam cesium vapor magnetometers. Additionally, four fluxgate magnetometers were used for vector measurements of the total field. The dataset also contains supplemental sensor data from the inertial navigation system, GPS position data, voltages, currents, and more.

During the data collection flights, various events were purposely carried out to cause temporal magnetic field disturbances. This included control surface movements (e.g., flaps up/down), fuel pump on/off, radio use, and movement of magnetic materials within the cabin. The flight patterns and altitudes were also varied from flight to flight to provide a diverse dataset. Please see the provided datasheet for further high-level dataset information and the readmes for individual flight details.

As of release v3 this data includes both year 1 of the collection (Flights 1002-1007) and year 2 of the collection (Flights 2001-2017) which correspond to 2020 and 2021 respectively. The zip files that are now available include information about the various fields available in each collection with the flight specific readmes including flight plan information (survey line vs transit, etc).

This dataset supports the Signal Enhancement for Magnetic Navigation Challenge Problem: https://magnav.mit.edu
DOI: 10.5281/zenodo.4271804
title: Signal Enhancement for Magnetic Navigation Challenge Problem

description: Harnessing the magnetic field of the earth for navigation has shown promise as a viable alternative to other navigation systems. A magnetic navigation system collects its own magnetic field data using a magnetometer and uses magnetic anomaly maps to determine the current location. The greatest challenge with magnetic navigation arises when the magnetic field data from the magnetometer on the navigation system encompass the magnetic field from not just the earth, but also from the vehicle on which it is mounted. It is difficult to separate the earth magnetic anomaly field magnitude, which is crucial for navigation, from the total magnetic field magnitude reading from the sensor. The purpose of this challenge problem is to decouple the earth and aircraft magnetic signals in order to derive a clean signal from which to perform magnetic navigation. Baseline testing on the dataset shows that the earth magnetic field can be extracted from the total magnetic field using machine learning (ML). The challenge is to remove the aircraft magnetic field from the total magnetic field using a trained neural network. These challenges offer an opportunity to construct an effective neural network for removing the aircraft magnetic field from the dataset, using an ML algorithm integrated with physics of magnetic navigation.
DOI: 10.5281/zenodo.6327685
title: DAF-MIT AIA Open Flight Data for Magnetic Navigation Research

description: This dataset was developed as part of the DAF-MIT Artificial Intelligence Accelerator to support research on airborne magnetic anomaly navigation (MagNav), an alternative to GPS. Flight data was collected during the summer of 2020 by Sander Geophysics Ltd. (SGL) near Ottawa, Ontario, Canada using a Cessna Grand Caravan equipped with a number of sensors. Within the dataset is a nearly perfect signal of the Earth's magnetic field (minimal aircraft interference) from tail stinger (boom) measurements, as well as four noisy magnetic signals (varying degrees of aircraft interference) from in-aircraft measurements. These scalar measurements of the total field were generated from five optically pumped, split-beam cesium vapor magnetometers. Additionally, four fluxgate magnetometers were used for vector measurements of the total field. The dataset also contains supplemental sensor data from the inertial navigation system, GPS position data, voltages, currents, and more. During the data collection flights, various events were purposely carried out to cause temporal magnetic field disturbances. This included control surface movements (e.g., flaps up/down), fuel pump on/off, radio use, and movement of magnetic materials within the cabin. The flight patterns and altitudes were also varied from flight to flight to provide a diverse dataset. Please see the provided datasheet for further high-level dataset information and the readmes for individual flight details. This dataset supports the Signal Enhancement for Magnetic Navigation Challenge Problem: https://magnav.mit.edu
DOI: 10.15468/dl.fmudrs
title: Occurrence Download

description: A dataset listing the 3303337 species recorded in GBIF matching the query:
{ }

 The dataset's 3303337 records were derived from 32249 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0139411-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tqjd5x
title: Occurrence Download

description: A dataset containing 5899 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Crassocephalum crepidioides (Benth.) S.Moore"
 ]
}

 The dataset includes 5899 records from 163 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0283828-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.geyxdw
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Getulaspis bupleuri (Marchal, 1904)",
 {
 "not" : {
 "DatasetKey" : [
 "is Global database of alien macrofungi"
 ]
 }
 },
 {
 "or" : [
 "Country is United States of America",
 "Country is United States",
 "Country is United States of America",
 "Country is Canada",
 "Continent is North America"
 ]
 }
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0367861-210914110416597/datasets/export for details.
DOI: 10.15468/dl.znatfx
title: Occurrence Download

description: A dataset containing 26 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Xanthosoma riparium E.G.Gonç."
 ]
}

 The dataset includes 26 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034740-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dfra25
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Harpiola Thomas, 1915)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((66 40,154 40,154 60,66 60,66 40))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1990"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0117984-230224095556074/datasets/export for details.
DOI: 10.15468/dl.d92szp
title: Occurrence Download

description: A dataset containing 576 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Anisorus quercus Goeze, 1783, Stenocorus quercus (Götz, 1783), Stenocorus quercus (Götz, 1783), Anisus septemgyratus (Rossmässler, 1835))",
 "Geometry POLYGON((-9.36035 44.71551,-10.59082 42.81152,-11.82129 36.80928,-7.69043 36.17336,-3.38379 35.88905,3.12012 38.13456,9.18457 38.20366,11.7334 37.16032,12.78809 34.74161,17.09473 33.79741, 23.15918 34.23451,30.10254 32.62087,33.2666 32.99024,35.72754 35.03,33.00293 35.53223,28.69629 35.17381,28.34473 36.31513,25.7959 37.50973,24.91699 39.90974,28.78418 40.6473,30.71777 41.17865,36.87012 45.213,38.18848 46.98025,38.71582 47.7541,39.94629 47.93107,40.20996 49.61071,37.0459 50.34546,35.72754 50.40152,33.79395 52.26816,31.68457 51.94426,31.4209 53.27835,32.56348 53.43572,30.98145 54.77535,30.89355 55.52863,28.43262 56.02295,27.20215 57.65716,27.37793 58.30949,27.90527 59.17593,29.66309 59.88894,27.6416 60.58697,31.50879 62.75473,28.78418 69.83962,30.89355 70.28912,29.22363 71.55274,21.75293 71.30079,14.28223 70.14036,11.38184 67.47492,4.87793 63.66576,-5.53711 71.52491,-10.63477 71.69129,-21.5332 67.74276,-28.56445 65.36684,-24.3457 61.35461,-9.36035 44.71551))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2021"
 ]
}

 The dataset includes 576 records from 50 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0230695-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cg9fud
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Canavalia makahaensis E.P.St.John"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0117988-230224095556074/datasets/export for details.
DOI: 10.15468/dl.jj7x7x
title: Occurrence Download

description: A dataset containing 421 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Stenocorus quercus (Götz, 1783), Stenocorus quercus (Götz, 1783), Anisus septemgyratus (Rossmässler, 1835))",
 "Geometry POLYGON((-9.36035 44.71551,-10.59082 42.81152,-11.82129 36.80928,-7.69043 36.17336,-3.38379 35.88905,3.12012 38.13456,9.18457 38.20366,11.7334 37.16032,12.78809 34.74161,17.09473 33.79741, 23.15918 34.23451,30.10254 32.62087,33.2666 32.99024,35.72754 35.03,33.00293 35.53223,28.69629 35.17381,28.34473 36.31513,25.7959 37.50973,24.91699 39.90974,28.78418 40.6473,30.71777 41.17865,36.87012 45.213,38.18848 46.98025,38.71582 47.7541,39.94629 47.93107,40.20996 49.61071,37.0459 50.34546,35.72754 50.40152,33.79395 52.26816,31.68457 51.94426,31.4209 53.27835,32.56348 53.43572,30.98145 54.77535,30.89355 55.52863,28.43262 56.02295,27.20215 57.65716,27.37793 58.30949,27.90527 59.17593,29.66309 59.88894,27.6416 60.58697,31.50879 62.75473,28.78418 69.83962,30.89355 70.28912,29.22363 71.55274,21.75293 71.30079,14.28223 70.14036,11.38184 67.47492,4.87793 63.66576,-5.53711 71.52491,-10.63477 71.69129,-21.5332 67.74276,-28.56445 65.36684,-24.3457 61.35461,-9.36035 44.71551))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2021"
 ]
}

 The dataset includes 421 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0230697-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.52chx3
title: Occurrence Download

description: A dataset containing 819285 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Agrostis capillaris L.",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 819285 records from 1556 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0117978-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4238aj
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Equisetum arvense",
 "Country is Brazil",
 "HasCoordinate is true"
 ]
}

 The dataset includes 20 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055346-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hptg6s
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Equisetum arvense",
 "Country is Iran (Islamic Republic of)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 8 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055347-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34816/ifao.archives.120472
title: NÉCROPOLE THÉBAINE_nu_2007_02159

description: Référence : nu_2007_02159<br />Site : Dra Abou el-Naga<br />Secteur : Chapelle (TT_13 (Churoy)); TT_13 (Churoy)<br />Type : photographie<br />
DOI: 10.15468/dl.gbaek7
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Oxytropis rosea Bunge"
 ]
}

 The dataset includes 14 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0139365-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34816/ifao.archives.120473
title: NÉCROPOLE THÉBAINE_nu_2007_02266

description: Référence : nu_2007_02266<br />Site : Cheikh Abd el-Gourna<br />Secteur : Chapelle (TT_318 (Amenmes)); TT_318 (Amenmes)<br />Type : photographie<br />
DOI: 10.15468/dl.a57jc7
title: Occurrence Download

description: A dataset containing 37 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eleutherodactylus grandis (Dixon, 1957)"
 ]
}

 The dataset includes 37 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0119632-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nbpy62
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pachydactylus parascutatus Bauer, Lamb & Branch, 2002"
 ]
}

 The dataset includes 20 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0292957-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34816/ifao.archives.120474
title: NÉCROPOLE THÉBAINE_nu_2007_02264

description: Référence : nu_2007_02264<br />Site : Dra Abou el-Naga<br />Secteur : Chapelle (TT_285 (Iny)); TT_285 (Iny)<br />Type : photographie<br />