cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10995109
title: Proteome-wide Prediction of the Functional Impact of Missense Variants with ProteoCast

description: Proteome-wide Prediction of the Functional Impact of Missense Variants with ProteoCast

This dataset contains mutation effect predictions for 22,169 Drosophila melanogaster protein isoforms, classifying over 293 million amino acid substitutions as neutral, uncertain, or impactful. The predictions were generated using the evolution-based GEMME model (E.Laine et al. MBE 2019) with multiple sequence alignments (MSAs) from the highly efficient ColabFold protocol (M.Mirdita et al. NatMet 2022, Abakarova et al. GBE 2023). To ensure reliability, we provide global (per-protein) and local (per-residue) confidence metrics, since the predictions are sensitive to the input MSA quality.

Predictions were validated using natural polymorphisms from the Drosophila Genetic Reference Panel (DGRP) and Drosophila Evolution over Space and Time (DEST2) datasets, as well as FlyBase’s developmentally lethal and hypomorphic mutations. Additionally, the dataset includes sensitivity data for post-translational modifications (PTMs) and short linear motifs (SLiMs), aiding functional site identification.

All this data can be visualized at proteocast.ijm.fr.  

Readme:



Drosophila_ProteoCast.tar.gz - this archive contains ProteoCast predictions and analysis for each unique proteoform, with folder names corresponding to IDs listed in the mapping_database.csv file. A detailed description of the folder structure and contents can be found in ReadMe.txt. 

data.tar.gz - this archive contains the data used in this study, sourced from FlyBase, DGRP2, and DEST2.

csv.tar.gz - this archive contains the files generated in this study. A detailed description of the folder structure and contents can be found in ReadMe.txt

ClinVar_data_analysis.tar.gz - this archive contains per-protein ProteoCast predictions for the ClinVar dataset of missense variants taken from ProteinGym.

CAID3_data_analysis.tar.gz - this archive contains the results of the analyses performed on the CAID3 benchmark datasets, including variant effect predictions and performance metrics used to evaluate ProteoCast on independent binding-related datasets.

PhyloHMM_data_analysis.tar.gz - this archive contains the PhyloHMM yeast binding-site dataset, along with the corresponding ProteoCast predictions and performance evaluations.
DOI: 10.15468/dl.ygtwc9
title: Occurrence Download

description: A dataset containing 1325 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is France",
 "DatasetKey is one of (iNaturalist Research-grade Observations, Monthly mosquito sampling in Montpellier (Occitanie), France, 2023, Prospections du moustique tigre menées par les agents du service démoustication du Département de la Charente-Maritime-Récoltes des pièges pondoirs)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Aedes albopictus",
 "Year 2007-2025"
 ]
}

 The dataset includes 1325 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013800-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.swsvgp
title: Occurrence Download

description: A dataset containing 944 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Svalbard and Jan Mayen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Ursus maritimus"
 ]
}

 The dataset includes 944 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013801-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.frgvty
title: Occurrence Download

description: A dataset containing 178 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ticherra acte"
 ]
}

 The dataset includes 178 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013799-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/cc4l1mc
title: CCDC 136512: Experimental Crystal Structure Determination

description: Related Article: J.A.R.Schmidt, J.Arnold|1999|Chem.Commun.||2149|doi:10.1039/a905620c
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/cc4l1nd
title: CCDC 136513: Experimental Crystal Structure Determination

description: Related Article: J.A.R.Schmidt, J.Arnold|1999|Chem.Commun.||2149|doi:10.1039/a905620c
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/cc4l1qg
title: CCDC 136515: Experimental Crystal Structure Determination

description: Related Article: H.Akdas, E.Graf, M.W.Hosseini, P.Rao, A.De Cian|2002|J.Supramol.Chem.|2|21|doi:10.1016/S1472-7862(02)00069-2
description: Related Article: P.Rao, M.W.Hosseini, A.De Cian, J.Fischer|1999|Chem.Commun.||2169|doi:10.1039/a906058h
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/cc4l1vl
title: CCDC 136519: Experimental Crystal Structure Determination

description: Related Article: L.Bonomo, E.Solari, R.Scopelliti, M.Latronico, C.Floriani|1999|Chem.Commun.||2227|doi:10.1039/a906817a
description: Related Article: L.Bonomo, E.Solari, R.Scopelliti, C.Floriani, N.Re|2000|J.Am.Chem.Soc.|122|5312|doi:10.1021/ja000253s
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/cc4l1wm
title: CCDC 136520: Experimental Crystal Structure Determination

description: Related Article: L.Bonomo, E.Solari, R.Scopelliti, M.Latronico, C.Floriani|1999|Chem.Commun.||2227|doi:10.1039/a906817a
description: Related Article: L.Bonomo, E.Solari, R.Scopelliti, C.Floriani, N.Re|2000|J.Am.Chem.Soc.|122|5312|doi:10.1021/ja000253s
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.r3auxp
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Brachiaria ramosa",
 "Country is United States of America",
 "HasCoordinate is true"
 ]
}

 The dataset includes 17 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007872-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/cc3tg0c
title: CCDC 113832: Experimental Crystal Structure Determination

description: Related Article: S.Gourbatsis, S.P.Perlepes, I.S.Butler, N.Hadjiliadis|1999|Polyhedron|18|2369|doi:10.1016/S0277-5387(99)00141-2
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/cc4l1k9
title: CCDC 136510: Experimental Crystal Structure Determination

description: Related Article: A.S.Weller, C.D.Andrews, A.D.Burrows, M.Green, J.M.Lynam, M.F.Mahon, C.Jones|1999|Chem.Commun.||2147|doi:10.1039/a905240b
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/cc3sg5h
title: CCDC 112876: Experimental Crystal Structure Determination

description: Related Article: J.Manzur, A.M.Garcia, A.Vega, E.Spodine|1999|Polyhedron|18|2399|doi:10.1016/S0277-5387(99)00136-9
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/cc3t7rw
title: CCDC 113638: Experimental Crystal Structure Determination

description: Related Article: S.N.Rao, K.N.Munshi, N.N.Rao, M.M.Bhadbhade, E.Suresh|1999|Polyhedron|18|2491|doi:10.1016/S0277-5387(99)00139-4
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/cc3g58z
title: CCDC 102990: Experimental Crystal Structure Determination

description: Related Article: A.Mentes, R.D.W.Kemmitt, J.Fawcett, D.R.Russeli|1999|Polyhedron|18|1141|doi:10.1016/S0277-5387(98)00404-5
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/cc3g590
title: CCDC 102991: Experimental Crystal Structure Determination

description: Related Article: A.Mentes, R.D.W.Kemmitt, J.Fawcett, D.R.Russeli|1999|Polyhedron|18|1141|doi:10.1016/S0277-5387(98)00404-5
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/cc3g5b1
title: CCDC 102992: Experimental Crystal Structure Determination

description: Related Article: A.Mentes, R.D.W.Kemmitt, J.Fawcett, D.R.Russeli|1999|Polyhedron|18|1141|doi:10.1016/S0277-5387(98)00404-5
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/cc4l1h7
title: CCDC 136508: Experimental Crystal Structure Determination

description: Related Article: A.D.Allen, B.Cheng, M.H.Fenwick, Wen-wei Huang, S.Missiha, D.Tahmassebi, T.T.Tidwell|1999|Org.Lett.|1|693|doi:10.1021/ol990628i
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/cc4kn8l
title: CCDC 136129: Experimental Crystal Structure Determination

description: Related Article: Jun Ho Shin, G.Parkin|1999|Inorg.Chem.Commun.|2|428|doi:10.1016/S1387-7003(99)00114-8
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/cc4kzxk
title: CCDC 136459: Experimental Crystal Structure Determination

description: Related Article: T.Takeda, T.Imamoto|1999|Tetrahedron:Asymm.|10|3209|doi:10.1016/S0957-4166(99)00325-0
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/cc4h2g4
title: CCDC 133655: Experimental Crystal Structure Determination

description: Related Article: A.Taher, A.M.Z.Slawin, G.W.Weaver|1999|Tetrahedron Lett.|40|8157|doi:10.1016/S0040-4039(99)01681-0
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/cc4kzyl
title: CCDC 136460: Experimental Crystal Structure Determination

description: Related Article: T.Takeda, T.Imamoto|1999|Tetrahedron:Asymm.|10|3209|doi:10.1016/S0957-4166(99)00325-0
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/cc4h2h5
title: CCDC 133656: Experimental Crystal Structure Determination

description: Related Article: A.Taher, A.M.Z.Slawin, G.W.Weaver|1999|Tetrahedron Lett.|40|8157|doi:10.1016/S0040-4039(99)01681-0
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/cc4h2j6
title: CCDC 133657: Experimental Crystal Structure Determination

description: Related Article: A.Taher, A.M.Z.Slawin, G.W.Weaver|1999|Tetrahedron Lett.|40|8157|doi:10.1016/S0040-4039(99)01681-0
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/cc3v9gp
title: CCDC 114652: Experimental Crystal Structure Determination

description: Related Article: R.Dilshad, K.M.Hanif, M.B.Hursthouse, S.E.Kabir, K.M.A.Malik, E.Rosenberg|1999|J.Organomet.Chem.|585|100|doi:10.1016/S0022-328X(99)00201-6
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/cc3v9hq
title: CCDC 114653: Experimental Crystal Structure Determination

description: Related Article: R.Dilshad, K.M.Hanif, M.B.Hursthouse, S.E.Kabir, K.M.A.Malik, E.Rosenberg|1999|J.Organomet.Chem.|585|100|doi:10.1016/S0022-328X(99)00201-6
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.7kjwq3
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Brachiaria ramosa",
 "Country is Mauritius",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007870-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/cc3w6kq
title: CCDC 115523: Experimental Crystal Structure Determination

description: Related Article: R.Papp, F.B.Somoza Junior, J.Sieler, S.Blaurock, E.Hey-Hawkins|1999|J.Organomet.Chem.|585|127|doi:10.1016/S0022-328X(99)00204-1
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/cc3w6lr
title: CCDC 115524: Experimental Crystal Structure Determination

description: Related Article: R.Papp, F.B.Somoza Junior, J.Sieler, S.Blaurock, E.Hey-Hawkins|1999|J.Organomet.Chem.|585|127|doi:10.1016/S0022-328X(99)00204-1
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/cc3w6ms
title: CCDC 115525: Experimental Crystal Structure Determination

description: Related Article: R.Papp, F.B.Somoza Junior, J.Sieler, S.Blaurock, E.Hey-Hawkins|1999|J.Organomet.Chem.|585|127|doi:10.1016/S0022-328X(99)00204-1
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/cc3wth8
title: CCDC 116110: Experimental Crystal Structure Determination

description: Related Article: A.V.Khvostov, B.M.Bulychev, V.K.Belsky, A.I.Sizov|1999|J.Organomet.Chem.|584|164|doi:10.1016/S0022-328X(99)00128-X
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/cc3wtkb
title: CCDC 116112: Experimental Crystal Structure Determination

description: Related Article: A.V.Khvostov, B.M.Bulychev, V.K.Belsky, A.I.Sizov|1999|J.Organomet.Chem.|584|164|doi:10.1016/S0022-328X(99)00128-X
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.4kfecg
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Brachiaria ramosa",
 "Country is Timor-Leste",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007871-251009101135966/datasets/export for details.
DOI: 10.5517/cc3s00w
title: CCDC 112437: Experimental Crystal Structure Determination

description: Related Article: O.E.Woisetschlager, K.Sunkel, W.Weigand, W.Beck|1999|J.Organomet.Chem.|584|122|doi:10.1016/S0022-328X(99)00107-2
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/cc3wtj9
title: CCDC 116111: Experimental Crystal Structure Determination

description: Related Article: A.V.Khvostov, B.M.Bulychev, V.K.Belsky, A.I.Sizov|1999|J.Organomet.Chem.|584|164|doi:10.1016/S0022-328X(99)00128-X
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/cc3rzyr
title: CCDC 112435: Experimental Crystal Structure Determination

description: Related Article: O.E.Woisetschlager, K.Sunkel, W.Weigand, W.Beck|1999|J.Organomet.Chem.|584|122|doi:10.1016/S0022-328X(99)00107-2
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/cc3rzzs
title: CCDC 112436: Experimental Crystal Structure Determination

description: Related Article: O.E.Woisetschlager, K.Sunkel, W.Weigand, W.Beck|1999|J.Organomet.Chem.|584|122|doi:10.1016/S0022-328X(99)00107-2
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.