Cite the Following Article
Leveraging glycomics data in glycoprotein 3D structure validation with Privateer
Haroldas Bagdonas, Daniel Ungar and Jon Agirre
Beilstein J. Org. Chem. 2020, 16, 2523–2533.
https://doi.org/10.3762/bjoc.16.204
How to Cite
Bagdonas, H.; Ungar, D.; Agirre, J. Beilstein J. Org. Chem. 2020, 16, 2523–2533. doi:10.3762/bjoc.16.204
Download Citation
Citation data can be downloaded as file using the "Download" button or used for copy/paste from the text window
below.
Citation data in RIS format can be imported by all major citation management software, including EndNote,
ProCite, RefWorks, and Zotero.
Presentation Graphic
| Picture with graphical abstract, title and authors for social media postings and presentations. | ||
| Format: PNG | Size: 11.0 MB | Download |
Citations to This Article
Up to 20 of the most recent references are displayed here.
Scholarly Works
- Elaphatha, A. C.; Ediriweera, M. K. An Idea to Explore: Analysis of Datasets on Diseases Associated With Protein Glycosylation as a Pedagogical Approach Using Free Software to Teach the Biochemistry of Diseases. Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology 2025, 53, 463–477. doi:10.1002/bmb.21909
- Dialpuri, J. S.; Bagdonas, H.; Schofield, L. C.; Pham, P. T.; Holland, L.; Agirre, J. Monitoring carbohydrate 3D structure quality with the Privateer database. Beilstein journal of organic chemistry 2024, 20, 931–939. doi:10.3762/bjoc.20.83
- Dialpuri, J. S.; Bagdonas, H.; Schofield, L. C.; Pham, P. T.; Holland, L.; Bond, P. S.; Sánchez Rodríguez, F.; McNicholas, S. J.; Agirre, J. Online carbohydrate 3D structure validation with the Privateer web app. Acta crystallographica. Section F, Structural biology communications 2024, 80, 30–35. doi:10.1107/s2053230x24000359
- Sharma, V.; Singh, A.; Chauhan, S.; Sharma, P. K.; Chaudhary, S.; Sharma, A.; Porwal, O.; Fuloria, N. K. Role of Artificial Intelligence in Drug Discovery and Target Identification in Cancer. Current drug delivery 2024, 21, 870–886. doi:10.2174/1567201821666230905090621
- Agirre, J.; Atanasova, M.; Bagdonas, H.; Ballard, C. B.; Baslé, A.; Beilsten-Edmands, J.; Borges, R. J.; Brown, D. G.; Burgos-Mármol, J. J.; Berrisford, J. M.; Bond, P. S.; Caballero, I.; Catapano, L.; Chojnowski, G.; Cook, A. G.; Cowtan, K. D.; Croll, T. I.; Debreczeni, J. É.; Devenish, N. E.; Dodson, E. J.; Drevon, T. R.; Emsley, P.; Evans, G.; Evans, P. R.; Fando, M.; Foadi, J.; Fuentes-Montero, L.; Garman, E. F.; Gerstel, M.; Gildea, R. J.; Hatti, K.; Hekkelman, M. L.; Heuser, P.; Hoh, S. W.; Hough, M. A.; Jenkins, H. T.; Jiménez, E.; Joosten, R. P.; Keegan, R. M.; Keep, N.; Krissinel, E. B.; Kolenko, P.; Kovalevskiy, O.; Lamzin, V. S.; Lawson, D. M.; Lebedev, A. A.; Leslie, A. G. W.; Lohkamp, B.; Long, F.; Malý, M.; McCoy, A. J.; McNicholas, S. J.; Medina, A.; Millán, C.; Murray, J. W.; Murshudov, G. N.; Nicholls, R. A.; Noble, M. E. M.; Oeffner, R.; Pannu, N. S.; Parkhurst, J. M.; Pearce, N.; Pereira, J.; Perrakis, A.; Powell, H. R.; Read, R. J.; Rigden, D. J.; Rochira, W.; Sammito, M.; Sánchez Rodríguez, F.; Sheldrick, G. M.; Shelley, K. L.; Simkovic, F.; Simpkin, A. J.; Skubak, P.; Sobolev, E.; Steiner, R. A.; Stevenson, K.; Tews, I.; Thomas, J. M. H.; Thorn, A.; Valls, J. T.; Uski, V.; Usón, I.; Vagin, A.; Velankar, S.; Vollmar, M.; Walden, H.; Waterman, D.; Wilson, K. S.; Winn, M. D.; Winter, G.; Wojdyr, M.; Yamashita, K. The CCP4 suite: integrative software for macromolecular crystallography. Acta crystallographica. Section D, Structural biology 2023, 79, 449–461. doi:10.1107/s2059798323003595
- Dialpuri, J. S.; Bagdonas, H.; Atanasova, M.; Schofield, L. C.; Hekkelman, M. L.; Joosten, R. P.; Agirre, J. Analysis and validation of overall N-glycan conformation in Privateer. Acta crystallographica. Section D, Structural biology 2023, 79, 462–472. doi:10.1107/s2059798323003510
- Joseph, A. P.; Malhotra, S.; Burnley, T.; Winn, M. D. Overview and applications of map and model validation tools in the CCP-EM software suite. Faraday discussions 2022, 240, 196–209. doi:10.1039/d2fd00103a
- Krawczyk, L.; Semwal, S.; Soubhye, J.; Lemri Ouadriri, S.; Prévost, M.; Van Antwerpen, P.; Roos, G.; Bouckaert, J. Native glycosylation and binding of the antidepressant paroxetine in a low-resolution crystal structure of human myeloperoxidase. Acta crystallographica. Section D, Structural biology 2022, 78, 1099–1109. doi:10.1107/s2059798322007082
- Lubbe, L.; Sewell, B. T.; Woodward, J. D.; Sturrock, E. D. Cryo-EM reveals mechanisms of angiotensin I-converting enzyme allostery and dimerization. The EMBO journal 2022, 41, e110550. doi:10.15252/embj.2021110550
- Perez, S.; Makshakova, O. Multifaceted Computational Modeling in Glycoscience. Chemical reviews 2022, 122, 15914–15970. doi:10.1021/acs.chemrev.2c00060
- Carpenter, E. J.; Seth, S.; Yue, N.; Greiner, R.; Derda, R. GlyNet: a multi-task neural network for predicting protein-glycan interactions. Chemical science 2022, 13, 6669–6686. doi:10.1039/d1sc05681f
- Atanasova, M.; Nicholls, R. A.; Joosten, R. P.; Agirre, J. Updated restraint dictionaries for carbohydrates in the pyranose form. Acta crystallographica. Section D, Structural biology 2022, 78, 455–465. doi:10.1107/s2059798322001103
- de Brevern, A. G.; Rebehmed, J. Current status of PTMs structural databases: applications, limitations and prospects. Amino acids 2022, 54, 575–590. doi:10.1007/s00726-021-03119-z
- Joosten, R. P.; Nicholls, R. A.; Agirre, J. Towards Consistency in Geometry Restraints for Carbohydrates in the Pyranose form: Modern Dictionary Generators Reviewed. Current medicinal chemistry 2022, 29, 1193–1207. doi:10.2174/0929867328666210902140754
- Aoki-Kinoshita, K. F.; Lisacek, F.; Karlsson, N.; Kolarich, D.; Packer, N. H. GlycoBioinformatics. Beilstein journal of organic chemistry 2021, 17, 2726–2728. doi:10.3762/bjoc.17.184
- Bagdonas, H.; Fogarty, C. A.; Fadda, E.; Agirre, J. The case for post-predictional modifications in the AlphaFold Protein Structure Database. Nature structural & molecular biology 2021, 28, 869–870. doi:10.1038/s41594-021-00680-9
- Pérez, S.; Bonnardel, F.; Lisacek, F.; Imberty, A.; Blum, S. R.; Makshakova, O. GAG-DB, the New Interface of the Three-Dimensional Landscape of Glycosaminoglycans. Biomolecules 2020, 10, 1660. doi:10.3390/biom10121660
- Scherbinina, S. I.; Toukach, P. V. Three-Dimensional Structures of Carbohydrates and Where to Find Them. International journal of molecular sciences 2020, 21, 7702. doi:10.3390/ijms21207702