cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.16841065
title: Molecular Bonding and Adhesion Analysis Toolkit: Computational Models and Simulation Resources for Intermolecular Interaction Studies  Weber

description: This package provides a complete computational framework for modeling, analyzing, and visualizing molecular bonding and adhesion phenomena. It is designed for researchers, materials scientists, chemists, and engineers interested in understanding intermolecular forces, adhesion mechanics, and surface interaction energetics.

The toolkit includes Python-based modules, data files, and configuration templates for simulating bond formation, adhesion energy profiles, and molecular surface contact behavior under varying environmental conditions. Features include:





Bonding Models: Predict and evaluate chemical and physical bonding between molecular species.




Adhesion Simulations: Model surface adhesion forces across different material interfaces.




Parameterizable Inputs: Adjust molecular structures, environmental conditions (temperature, pressure, humidity), and surface characteristics for tailored simulations.




Data Analysis Utilities: Extract key metrics such as bond energy, adhesion coefficients, and equilibrium distances.




Visualization Tools: Generate plots and surface interaction maps for presentation or publication.




Extensible Framework: Modular design allows integration with other computational chemistry packages (e.g., LAMMPS, OpenBabel, RDKit).



Example scripts and documentation are included to help users quickly set up simulations, modify parameters, and interpret results. This package supports research in adhesion science, biomaterials, nanotechnology, coatings, and molecular engineering.
DOI: 10.5281/zenodo.16841066
title: Molecular Bonding and Adhesion Analysis Toolkit: Computational Models and Simulation Resources for Intermolecular Interaction Studies  Weber

description: This package provides a complete computational framework for modeling, analyzing, and visualizing molecular bonding and adhesion phenomena. It is designed for researchers, materials scientists, chemists, and engineers interested in understanding intermolecular forces, adhesion mechanics, and surface interaction energetics.

The toolkit includes Python-based modules, data files, and configuration templates for simulating bond formation, adhesion energy profiles, and molecular surface contact behavior under varying environmental conditions. Features include:





Bonding Models: Predict and evaluate chemical and physical bonding between molecular species.




Adhesion Simulations: Model surface adhesion forces across different material interfaces.




Parameterizable Inputs: Adjust molecular structures, environmental conditions (temperature, pressure, humidity), and surface characteristics for tailored simulations.




Data Analysis Utilities: Extract key metrics such as bond energy, adhesion coefficients, and equilibrium distances.




Visualization Tools: Generate plots and surface interaction maps for presentation or publication.




Extensible Framework: Modular design allows integration with other computational chemistry packages (e.g., LAMMPS, OpenBabel, RDKit).



Example scripts and documentation are included to help users quickly set up simulations, modify parameters, and interpret results. This package supports research in adhesion science, biomaterials, nanotechnology, coatings, and molecular engineering.
DOI: 10.3535/153-7w7-g7d
title: Pinna saccata Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/jwr-etv-tjl
title: Satsuma caliginosa (A. Adams & Reeve, 1850)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/069-bys-q9n
title: Atrina pectinata (Linnaeus, 1767)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/xev-0dm-xx9
title: Ostreidae Rafinesque, 1815

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/vlx-vz0-q1n
title: Pecten maximus (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.5281/zenodo.16753348
title: Diamond2GO Database – Version 2025-08-12 (nr_clean_d2go)

description: This is the updated Diamond2GO reference database built on 12th August 2025.

It is a DIAMOND-formatted protein database (`.dmnd`) consisting of over 27 million sequences derived from the NCBI `nr` dataset, filtered to include only those with Gene Ontology (GO) annotations, and redundancy reduction using MMseqs2 (95% similarity). This version improves sensitivity and annotation coverage compared to the original 2023 release used in the published D2GO manuscript, and the earlier 2025 release.

This database is intended for use with the Diamond2GO tool, which enables rapid GO-term annotation and enrichment analysis for high-throughput sequencing datasets.

For reproducibility of results published using the earlier version (699,409 sequences), please refer to the [v1.0.0 release] https://github.com/rhysf/Diamond2GO/releases/tag/6a035ce
DOI: 10.5281/zenodo.16818512
title: Diamond2GO Database – Version 2025-08-12 (nr_clean_d2go)

description: This is the updated Diamond2GO reference database built on 12th August 2025.

It is a DIAMOND-formatted protein database (`.dmnd`) consisting of over 27 million sequences derived from the NCBI `nr` dataset, filtered to include only those with Gene Ontology (GO) annotations, and redundancy reduction using MMseqs2 (95% similarity). This version improves sensitivity and annotation coverage compared to the original 2023 release used in the published D2GO manuscript, and the earlier 2025 release.

This database is intended for use with the Diamond2GO tool, which enables rapid GO-term annotation and enrichment analysis for high-throughput sequencing datasets.

For reproducibility of results published using the earlier version (699,409 sequences), please refer to the [v1.0.0 release] https://github.com/rhysf/Diamond2GO/releases/tag/6a035ce
DOI: 10.3535/3sz-mb7-xdy
title: Monacha cantiana (Montagu, 1803)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/5fx-52p-8rj
title: Conus ebraeus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.5281/zenodo.16838437
title: 001

description:
DOI: 10.3535/9he-ts4-m1m
title: Perforatella incarnata (O. F. Müller, 1774)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ykj-ye9-1z1
title: Oxyloma elegans (Risso, 1826)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.5281/zenodo.15471975
title: 001

description:
DOI: 10.3535/1vk-y8w-3rd
title: Euplecta imperforata Schepman, 1918

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/g86-mat-4f9
title: Hypselostyla evanescens (Broderip, 1841)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/dxt-v5v-yhy
title: Landouria Godwin-Austen, 1918

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/xz6-hpj-tew
title: Fruticicola fruticum (O. F. Müller, 1774)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/3sf-4kv-1bg
title: Discolucina virginea (Deshayes, 1832)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/laz-tg1-bj1
title: Byssogerdius subsulcatus (Dunker, 1857)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/plp-7gd-acb
title: Ctenoides ales (H. J. Finlay, 1927)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/4sb-a3q-216
title: Sagda alligans (C. B. Adams, 1850)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/74v-8d9-cby
title: Kurtiella bidentata (Montagu, 1803)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/s5x-wl8-a50
title: Magallana gigas (Thunberg, 1793)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.5517/cc4mtzj
title: CCDC 138228: Experimental Crystal Structure Determination

description: Related Article: T.Kawamura, H.Kachi, H.Fujii, C.Kachi-Terajima, Y.Kawamura, N.Kanematsu, M.Ebihara, K.Sugimoto, T.Kuroda-Sowa, M.Munakata|2000|Bull.Chem.Soc.Jpn.|73|657|doi:10.1246/bcsj.73.657
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/cc4ndv0
title: CCDC 138782: Experimental Crystal Structure Determination

description: Related Article: K.Sugimoto, T.Kuroda-Sowa, T.Goto, M.Maekawa, M.Munakata|2000|Bull.Chem.Soc.Jpn.|73|651|doi:10.1246/bcsj.73.651
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/cc4ndw1
title: CCDC 138783: Experimental Crystal Structure Determination

description: Related Article: K.Sugimoto, T.Kuroda-Sowa, T.Goto, M.Maekawa, M.Munakata|2000|Bull.Chem.Soc.Jpn.|73|651|doi:10.1246/bcsj.73.651
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/cc3l190
title: CCDC 106711: Experimental Crystal Structure Determination

description: Related Article: E.Fanghanel, H.Bartossek, Th.Lochter, U.Baumeister, H.Hartung|1997|J.Prakt.Chem.-Chem.-Zeitung|339|277|doi:10.1002/prac.19973390149
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/cc3llpy
title: CCDC 107250: Experimental Crystal Structure Determination

description: Related Article: E.Fanghanel, A.Hucke, U.Baumeister, H.Hartung|1996|J.Prakt.Chem.-Chem.-Zeitung|338|345|doi:10.1002/prac.19963380167
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/cc3llqz
title: CCDC 107251: Experimental Crystal Structure Determination

description: Related Article: E.Fanghanel, A.Hucke, U.Baumeister, H.Hartung|1996|J.Prakt.Chem.-Chem.-Zeitung|338|345|doi:10.1002/prac.19963380167
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/cc4w28b
title: CCDC 145181: Experimental Crystal Structure Determination

description: Related Article: G.B.Onoa, V.Moreno, M.Font-Bardia, X.Solans, J.M.Perez, C.Alonso|1999|J.Inorg.Biochem.|75|205|doi:10.1016/S0162-0134(99)00089-6
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/cc3hcdb
title: CCDC 104141: Experimental Crystal Structure Determination

description: Related Article: J.Ellermann, J.Schamberger, F.A.Knoch, M.Moll, W.Bauer|1997|Monatsh.Chem.|128|399|doi:10.1007/BF00810777
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/cc4lrn3
title: CCDC 137195: Experimental Crystal Structure Determination

description: Related Article: P.M.Lahti, B.Esat, J.R.Ferrer, Yanbing Liu, K.A.Marby, Chunping Xie, C.George, G.Antorrena, F.Palacio|1999|Mol.Cryst.Liq.Cryst.Sci.Technol.,Sect.A|334|285|doi:10.1080/10587259908023326
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/cc3z99n
title: CCDC 118491: Experimental Crystal Structure Determination

description: Related Article: W.Simanko, R.Schmid, K.Kirchner, K.Mereiter|1999|Monatsh.Chem.|130|1301|doi:10.1007/s007060050288
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/cc3z9bp
title: CCDC 118492: Experimental Crystal Structure Determination

description: Related Article: W.Simanko, R.Schmid, K.Kirchner, K.Mereiter|1999|Monatsh.Chem.|130|1301|doi:10.1007/s007060050288
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/cc3z9cq
title: CCDC 118493: Experimental Crystal Structure Determination

description: Related Article: W.Simanko, R.Schmid, K.Kirchner, K.Mereiter|1999|Monatsh.Chem.|130|1301|doi:10.1007/s007060050288
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/cc3z9dr
title: CCDC 118494: Experimental Crystal Structure Determination

description: Related Article: W.Simanko, R.Schmid, K.Kirchner, K.Mereiter|1999|Monatsh.Chem.|130|1301|doi:10.1007/s007060050288
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/cc4l955
title: CCDC 136746: Experimental Crystal Structure Determination

description: Related Article: S.Vijayalakshmi, R.B.Rao, I.L.Karle, P.Balaram|2000|Biopolymers|53|84|doi:10.1002/(SICI)1097-0282(200001)53:1<84::AID-BIP8>3.3.CO;2-N
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.u9g4ns
title: Occurrence Download

description: A dataset containing 156227 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 "year",
 IF(ISNULL(kingdomkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY kingdomkey, "year")) kingdomcount,
 IF(ISNULL(phylumkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY phylumkey, "year")) phylumcount,
 IF(ISNULL(classkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY classkey, "year")) classcount,
 IF(ISNULL(orderkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY orderkey, "year")) ordercount,
 IF(ISNULL(familykey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY familykey, "year")) familycount,
 IF(ISNULL(genuskey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY genuskey, "year")) genuscount,
 COUNT(*) occurrences,
 MIN(GBIF_TEMPORALUNCERTAINTY(eventdate, eventtime)) mintemporaluncertainty,
 MIN(COALESCE(coordinateuncertaintyinmeters, 1000)) mincoordinateuncertaintyinmeters
FROM
 occurrence
WHERE
 occurrence.countrycode = 'KR'
 AND occurrence.occurrencestatus = 'PRESENT'
 AND (occurrence."year" &gt;= 2001 AND occurrence."year" &lt;= 2025)
 AND occurrence.hasgeospatialissues = FALSE
 AND NOT GBIF_STRINGARRAYCONTAINS(occurrence.issue, 'TAXON_MATCH_FUZZY', TRUE)
 AND (occurrence.distancefromcentroidinmeters &gt;= 2000.0 OR occurrence.distancefromcentroidinmeters IS NULL)
 AND NOT occurrence.basisofrecord IN ('FOSSIL_SPECIMEN', 'LIVING_SPECIMEN')
 AND (occurrence.specieskey IS NOT NULL AND occurrence."year" IS NOT NULL)
GROUP BY
 occurrence.kingdom,
 occurrence.kingdomkey,
 occurrence.phylum,
 occurrence.phylumkey,
 occurrence.class,
 occurrence.classkey,
 occurrence."order",
 occurrence.orderkey,
 occurrence.family,
 occurrence.familykey,
 occurrence.genus,
 occurrence.genuskey,
 occurrence.species,
 occurrence.specieskey,
 occurrence."year"

 The dataset's 156227 records were derived from 673 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008405-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/cc4l966
title: CCDC 136747: Experimental Crystal Structure Determination

description: Related Article: S.Vijayalakshmi, R.B.Rao, I.L.Karle, P.Balaram|2000|Biopolymers|53|84|doi:10.1002/(SICI)1097-0282(200001)53:1<84::AID-BIP8>3.3.CO;2-N
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/cc3x7bk
title: CCDC 116508: Experimental Crystal Structure Determination

description: Related Article: Y.Yamada, N.Ueyama, T.Okamura, W.Mori, A.Nakamura|1998|Inorg.Chim.Acta|275|43|doi:10.1016/S0020-1693(97)06144-6
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/cc4w1lm
title: CCDC 145160: Experimental Crystal Structure Determination

description: Related Article: X.Riera, A.Caubet, C.Lopez, V.Moreno, X.Solans, M.Font-Bardia|2000|Organometallics|19|1384|doi:10.1021/om990602v
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/cc3hf11
title: CCDC 104192: Experimental Crystal Structure Determination

description: Related Article: D.Bartschat, S.Borner, A.Mosandl, J.W.Bats|1997|Z.Lebensm.-Unters.Forsch.A|205|76|doi:10.1007/s002170050127
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/cc3x79j
title: CCDC 116507: Experimental Crystal Structure Determination

description: Related Article: Y.Yamada, N.Ueyama, T.Okamura, W.Mori, A.Nakamura|1998|Inorg.Chim.Acta|275|43|doi:10.1016/S0020-1693(97)06144-6
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/cc4vnxj
title: CCDC 144798: Experimental Crystal Structure Determination

description: Related Article: R.D.Gilbertson, T.J.R.Weakley, M.M.Haley|2000|J.Org.Chem.|65|1422|doi:10.1021/jo9915372
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/cc4vnyk
title: CCDC 144799: Experimental Crystal Structure Determination

description: Related Article: R.D.Gilbertson, T.J.R.Weakley, M.M.Haley|2000|J.Org.Chem.|65|1422|doi:10.1021/jo9915372
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/cc4vnzl
title: CCDC 144800: Experimental Crystal Structure Determination

description: Related Article: R.D.Gilbertson, T.J.R.Weakley, M.M.Haley|2000|J.Org.Chem.|65|1422|doi:10.1021/jo9915372
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.