cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.16284914
title: MGMG: Cell Morphology-Guided Molecule Generation for Drug Discovery

description: This dataset supports MGMG (Morphology-Guided Molecule Generation), a phenotypic drug discovery-oriented framework that integrates morphological information from compound treatment with molecular textual descriptions to enable de novo molecule design without the need for target information. Please cite this publication when using the dataset:





MGMG: Cell Morphology-Guided Molecule Generation for Drug Discovery


Qiaosi Tang, Daoyun Ding, Xiaoyong Yuan, Gustavo Seabra, Peter A Ramdhan, Chi-Yuan Liu, My T. Thai, Chenglong Li, Hendrik Luesch, Yanjun Li

bioRxiv 2025.07.11.664424; doi: https://doi.org/10.1101/2025.07.11.664424


Overview

The dataset contains model checkpoint, input test data, and results required to reproduce MGMG’s evaluations and case studies, including the activator design task and docking task. It is structured to support reproducibility, downstream applications, and benchmarking by the research community. All data is organized under the archive file MGMG_dataset.zip.

Contents

checkpoint/





pytorch_model.bin: Saved checkpoint of the trained MGMG model.



testset_Morphology-BBBC036v1/





unique_morph_info.json: Morphological profiles for the test compounds, derived from Cell Painting images in BBBC036v1 (Bray et al. 2017) and processed using PyCytominer.



testset_Mol-Instructions-BBBC036v1/





task3_MolIns_text2mol_test_tk.json: Compound textual descriptions sourced from PubChem, aligned with the same compounds in the morphology set.



testset_MolCaptioned-BBBC036v1/





task3_MolIns_text2mol_test_tkgendesc_revised.json: Synthetic compound textual descriptions generated by BioT5, aligned with the same compounds in the morphology set.



activator_design/





task3_GeneOE_text2mol_test_[GENE].json: Textual descriptions for gene-specific molecule generation inputs, where each file corresponds to a gene overexpression case (e.g., TP53, BRCA1, NFKB1), with text profiles generated by GPT-4.0. Used for the first step of the activator design task (See the preprint Methods section for more details).




task3_GeneOEbiot5gen_test.json: BioT5-generated molecular descriptions for all gene perturbation cases. Used for the third step of the activator design task (See the preprint Methods section for more details).




unique_gene_morph_info.json: Morphological profiles of cells with gene overexpression perturbations, used for the activator design case study in the manuscript.



docking_files/





[PDB_ID].maegz: Prepared docking files (protein target, reference and generated sample compounds) for select demo cases (3CMF, 4E2J, 7DFP, 7QZ7), compatible with Maestro/PyMOL.
DOI: 10.15468/dl.n7pqtr
title: Occurrence Download

description: A dataset containing 2177041 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Grus grus)",
 "Country is one of (Åland Islands, Albania, Andorra, Austria, Belarus, Belgium, Bosnia and Herzegovina, Bulgaria, Croatia, Czechia, Denmark, Estonia, Faroe Islands, Finland, France, Germany, Gibraltar, Greece, Guernsey, Holy See, Hungary, Iceland, Ireland, Isle of Man, Italy, Jersey, Latvia, Liechtenstein, Lithuania, Luxembourg, Malta, Moldova, Republic of, Monaco, Montenegro, Netherlands, North Macedonia, Norway, Poland, Portugal, Romania, Russian Federation, San Marino, Serbia, Slovakia, Slovenia, Spain, Svalbard and Jan Mayen, Sweden, Switzerland, Ukraine, United Kingdom of Great Britain and Northern Ireland)"
 ]
}

 The dataset includes 2177041 records from 1372 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024481-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/cc4h62w
title: CCDC 133767: Experimental Crystal Structure Determination

description: Related Article: D.Sellmann, K.Engl, F.W.Heinemann, J.Sieler|2000|Eur.J.Inorg.Chem.|2000|1079|doi:10.1002/(SICI)1099-0682(200005)2000:5<1079::AID-EJIC1079>3.3.CO;2-M
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/cc3hxp5
title: CCDC 104677: Experimental Crystal Structure Determination

description: Related Article: K.Krohn, I.Terstiege, U.Florke|1998|J.Carbohydr.Chem.|17|197|doi:10.1080/07328309808002322
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/cc4vb6h
title: CCDC 144466: Experimental Crystal Structure Determination

description: Related Article: A.T.Gubaidullin, Y.E.Morozova, A.R.Mustafina, E.Kh.Kazakova, I.A.Litvinov, A.I.Konovalov|1999|Mendeleev Commun.|9|9|doi:10.1070/MC1999v009n01ABEH000978
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/cc3h0wg
title: CCDC 103815: Experimental Crystal Structure Determination

description: Related Article: G.Galley, B.Ziemer, M.Patzel|1998|J.Prakt.Chem.-Chem.-Zeitung|340|551|doi:10.1002/prac.19983400608
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/cc4n485
title: CCDC 138516: Experimental Crystal Structure Determination

description: Related Article: Chao-mei Ma, N.Nakamura, M.Hattori, H.Kakuda, Jun-chan Qiao, Hai-lan Yu|2000|J.Nat.Prod.|63|238|doi:10.1021/np9902441
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/cc4tb4d
title: CCDC 143503: Experimental Crystal Structure Determination

description: Related Article: A.P.Tamiz, Jianrong Zhang, J.L.Flippen-Anderson, Mei Zhang, K.M.Johnson, O.Deschaux, S.Tella, A.P.Kozikowski|2000|J.Med.Chem.|43|1215|doi:10.1021/jm9905561
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/cc4plcr
title: CCDC 139914: Experimental Crystal Structure Determination

description: Related Article: R.Klvana, R.Pohl, J.Pawlas, J.Cejka, H.Dvorakova, R.Hrabal, S.Bohm, B.Kratochvil, J.Kuthan|2000|Collect.Czech.Chem.Commun.|65|651|doi:10.1135/cccc20000651
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/cc4l10r
title: CCDC 136493: Experimental Crystal Structure Determination

description: Related Article: G.Hoshina, M.Tsuchimoto, S.Ohba|2000|Bull.Chem.Soc.Jpn.|73|369|doi:10.1246/bcsj.73.369
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/cc4l11s
title: CCDC 136494: Experimental Crystal Structure Determination

description: Related Article: G.Hoshina, M.Tsuchimoto, S.Ohba|2000|Bull.Chem.Soc.Jpn.|73|369|doi:10.1246/bcsj.73.369
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/cc4l12t
title: CCDC 136495: Experimental Crystal Structure Determination

description: Related Article: G.Hoshina, M.Tsuchimoto, S.Ohba|2000|Bull.Chem.Soc.Jpn.|73|369|doi:10.1246/bcsj.73.369
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/cc4l3qj
title: CCDC 136577: Experimental Crystal Structure Determination

description: Related Article: N.R.Sangeetha, S.Pal|2000|Bull.Chem.Soc.Jpn.|73|357|doi:10.1246/bcsj.73.357
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/cc4l3rk
title: CCDC 136578: Experimental Crystal Structure Determination

description: Related Article: N.R.Sangeetha, S.Pal|2000|Bull.Chem.Soc.Jpn.|73|357|doi:10.1246/bcsj.73.357
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/cc4l3sl
title: CCDC 136579: Experimental Crystal Structure Determination

description: Related Article: N.R.Sangeetha, S.Pal|2000|Bull.Chem.Soc.Jpn.|73|357|doi:10.1246/bcsj.73.357
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/cc3hrs3
title: CCDC 104525: Experimental Crystal Structure Determination

description: Related Article: J.Gindl, M.A.Said, Peihua Yu, H.W.Roesky, M.Noltemeyer, H.-G.Schmidt|1999|Isr.J.Chem.|39|125|doi:10.1002/ijch.199900014
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.ymu5uu
title: Occurrence Download

description: A dataset containing 82 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mentzelia springeri"
 ]
}

 The dataset includes 82 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008270-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15156/bio/sh0161827.10fu
title: SH0161827.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0161828.10fu
title: SH0161828.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0161829.10fu
title: SH0161829.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0161830.10fu
title: SH0161830.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.25549/usctheses-ouc11399n8fh
title: DISORDERED WITH A PURPOSE: CHARACTERIZING THE DYNAMIC FUZZY COAT OF Î±-SYNUCLEIN FIBRILS
DOI: 10.15156/bio/sh0161831.10fu
title: SH0161831.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0161832.10fu
title: SH0161832.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0161833.10fu
title: SH0161833.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0161834.10fu
title: SH0161834.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0161835.10fu
title: SH0161835.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.