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| # This CITATION.cff file was generated with cffinit. | ||
| # Visit https://bit.ly/cffinit to generate yours today! | ||
|
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| cff-version: 1.2.0 | ||
| doi: 10.5281/zenodo.6674124 | ||
| title: "DeepRank2: Mining 3D Protein Structures with Geometric Deep Learning" | ||
| message: >- | ||
| If you use this software, please cite it using the | ||
| metadata from this file. | ||
| type: software | ||
| cff-version: "1.2.0" | ||
| authors: | ||
| - given-names: Giulia | ||
| family-names: Crocioni | ||
| email: [email protected] | ||
| affiliation: Netherlands eScience Center, Amsterdam, The Netherlands | ||
| - family-names: Crocioni | ||
| given-names: Giulia | ||
| orcid: "https://orcid.org/0000-0002-0823-0121" | ||
| - family-names: Bodor | ||
| given-names: Dani L. | ||
| orcid: "https://orcid.org/0000-0003-2109-2349" | ||
| - family-names: Baakman | ||
| given-names: Coos | ||
| orcid: "https://orcid.org/0000-0003-4317-1566" | ||
| - family-names: Parizi | ||
| given-names: Farzaneh M. | ||
| orcid: "https://orcid.org/0000-0003-4230-7492" | ||
| - family-names: Rademaker | ||
| given-names: Daniel-T. | ||
| orcid: "https://orcid.org/0000-0003-1959-1317" | ||
| - family-names: Ramakrishnan | ||
| given-names: Gayatri | ||
| orcid: "https://orcid.org/0000-0001-8203-2783" | ||
| - family-names: Burg | ||
| given-names: Sven A. | ||
| name-particle: van der | ||
| orcid: "https://orcid.org/0000-0003-1250-6968" | ||
| - family-names: Marzella | ||
| given-names: Dario F. | ||
| orcid: "https://orcid.org/0000-0002-0043-3055" | ||
| - family-names: Teixeira | ||
| given-names: João M. C. | ||
| orcid: "https://orcid.org/0000-0002-9113-0622" | ||
| - family-names: Xue | ||
| given-names: Li C. | ||
| orcid: "https://orcid.org/0000-0002-2613-538X" | ||
| contact: | ||
| - family-names: Crocioni | ||
| given-names: Giulia | ||
| orcid: "https://orcid.org/0000-0002-0823-0121" | ||
| doi: 10.5281/zenodo.10566809 | ||
| message: If you use this software, please cite our article in the | ||
| Journal of Open Source Software. | ||
| preferred-citation: | ||
| authors: | ||
| - family-names: Crocioni | ||
| given-names: Giulia | ||
| orcid: "https://orcid.org/0000-0002-0823-0121" | ||
| - given-names: Dani L. | ||
| family-names: Bodor | ||
| email: [email protected] | ||
| affiliation: Netherlands eScience Center, Amsterdam, The Netherlands | ||
| - family-names: Bodor | ||
| given-names: Dani L. | ||
| orcid: "https://orcid.org/0000-0003-2109-2349" | ||
| - given-names: Coos | ||
| family-names: Baakman | ||
| affiliation: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands | ||
| - family-names: Baakman | ||
| given-names: Coos | ||
| orcid: "https://orcid.org/0000-0003-4317-1566" | ||
| - given-names: Farzaneh Meimandi | ||
| family-names: Parizi | ||
| affiliation: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands | ||
| - family-names: Parizi | ||
| given-names: Farzaneh M. | ||
| orcid: "https://orcid.org/0000-0003-4230-7492" | ||
| - given-names: Daniel-T. | ||
| family-names: Rademaker | ||
| affiliation: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands | ||
| - family-names: Rademaker | ||
| given-names: Daniel-T. | ||
| orcid: "https://orcid.org/0000-0003-1959-1317" | ||
| - given-names: Gayatri | ||
| family-names: Ramakrishnan | ||
| affiliation: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands | ||
| - family-names: Ramakrishnan | ||
| given-names: Gayatri | ||
| orcid: "https://orcid.org/0000-0001-8203-2783" | ||
| - given-names: Sven A. | ||
| family-names: van der Burg | ||
| affiliation: Netherlands eScience Center, Amsterdam, The Netherlands | ||
| - family-names: Burg | ||
| given-names: Sven A. | ||
| name-particle: van der | ||
| orcid: "https://orcid.org/0000-0003-1250-6968" | ||
| - given-names: Dario F. | ||
| family-names: Marzella | ||
| affiliation: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands | ||
| - family-names: Marzella | ||
| given-names: Dario F. | ||
| orcid: "https://orcid.org/0000-0002-0043-3055" | ||
| - given-names: João M.C. | ||
| family-names: Teixeira | ||
| affiliation: Independent Researcher | ||
| - family-names: Teixeira | ||
| given-names: João M. C. | ||
| orcid: "https://orcid.org/0000-0002-9113-0622" | ||
| - given-names: Li C. | ||
| family-names: Xue | ||
| affiliation: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands | ||
| - family-names: Xue | ||
| given-names: Li C. | ||
| orcid: "https://orcid.org/0000-0002-2613-538X" | ||
| abstract: >- | ||
| DeepRank2 is an open-source deep learning | ||
| framework for data mining of protein-protein interfaces | ||
| or single-residue variants. | ||
| keywords: | ||
| - Python | ||
| - PyTorch | ||
| - structural biology | ||
| - geometric deep learning | ||
| - 3D protein structures | ||
| - protein-protein interfaces | ||
| - single-residue variants | ||
| - graph neural networks | ||
| - convolutional neural networks | ||
| - DeepRank | ||
| license: Apache-2.0 | ||
| commit: 4e8823758ba03f824b4281f5689cb6a335ab2f6c | ||
| version: "3.0.1" | ||
| date-released: "2024-02-22" | ||
| date-published: 2024-02-27 | ||
| doi: 10.21105/joss.05983 | ||
| issn: 2475-9066 | ||
| issue: 94 | ||
| journal: Journal of Open Source Software | ||
| publisher: | ||
| name: Open Journals | ||
| start: 5983 | ||
| title: "DeepRank2: Mining 3D Protein Structures with Geometric Deep | ||
| Learning" | ||
| type: article | ||
| url: "https://joss.theoj.org/papers/10.21105/joss.05983" | ||
| volume: 9 | ||
| title: "DeepRank2: Mining 3D Protein Structures with Geometric Deep | ||
| Learning" |
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