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Monitoring carbohydrate 3D structure quality with the Privateer database.
Beilstein J Org Chem. 2024 Apr 24;20:931-939. doi: 10.3762/bjoc.20.83. eCollection 2024.
Beilstein J Org Chem. 2024.
PMID: 38711584
Free PMC article.
Online carbohydrate 3D structure validation with the Privateer web app.
Dialpuri JS, Bagdonas H, Schofield LC, Pham PT, Holland L, Bond PS, Sánchez Rodríguez F, McNicholas SJ, Agirre J.
Dialpuri JS, et al. Among authors: bagdonas h.
Acta Crystallogr F Struct Biol Commun. 2024 Feb 1;80(Pt 2):30-35. doi: 10.1107/S2053230X24000359. Epub 2024 Jan 24.
Acta Crystallogr F Struct Biol Commun. 2024.
PMID: 38265073
Free PMC article.
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The CCP4 suite: integrative software for macromolecular crystallography.
Agirre J, Atanasova M, Bagdonas H, Ballard CB, Baslé A, Beilsten-Edmands J, Borges RJ, Brown DG, Burgos-Mármol JJ, Berrisford JM, Bond PS, Caballero I, Catapano L, Chojnowski G, Cook AG, Cowtan KD, Croll TI, Debreczeni JÉ, Devenish NE, Dodson EJ, Drevon TR, Emsley P, Evans G, Evans PR, Fando M, Foadi J, Fuentes-Montero L, Garman EF, Gerstel M, Gildea RJ, Hatti K, Hekkelman ML, Heuser P, Hoh SW, Hough MA, Jenkins HT, Jiménez E, Joosten RP, Keegan RM, Keep N, Krissinel EB, Kolenko P, Kovalevskiy O, Lamzin VS, Lawson DM, Lebedev AA, Leslie AGW, Lohkamp B, Long F, Malý M, McCoy AJ, McNicholas SJ, Medina A, Millán C, Murray JW, Murshudov GN, Nicholls RA, Noble MEM, Oeffner R, Pannu NS, Parkhurst JM, Pearce N, Pereira J, Perrakis A, Powell HR, Read RJ, Rigden DJ, Rochira W, Sammito M, Sánchez Rodríguez F, Sheldrick GM, Shelley KL, Simkovic F, Simpkin AJ, Skubak P, Sobolev E, Steiner RA, Stevenson K, Tews I, Thomas JMH, Thorn A, Valls JT, Uski V, Usón I, Vagin A, Velankar S, Vollmar M, Walden H, Waterman D, Wilson KS, Winn MD, Winter G, Wojdyr M, Yamashita K.
Agirre J, et al. Among authors: bagdonas h.
Acta Crystallogr D Struct Biol. 2023 Jun 1;79(Pt 6):449-461. doi: 10.1107/S2059798323003595. Epub 2023 May 30.
Acta Crystallogr D Struct Biol. 2023.
PMID: 37259835
Free PMC article.
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Analysis and validation of overall N-glycan conformation in Privateer.
Dialpuri JS, Bagdonas H, Atanasova M, Schofield LC, Hekkelman ML, Joosten RP, Agirre J.
Dialpuri JS, et al. Among authors: bagdonas h.
Acta Crystallogr D Struct Biol. 2023 Jun 1;79(Pt 6):462-472. doi: 10.1107/S2059798323003510. Epub 2023 May 23.
Acta Crystallogr D Struct Biol. 2023.
PMID: 37219590
Free PMC article.
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The case for post-predictional modifications in the AlphaFold Protein Structure Database.
Bagdonas H, Fogarty CA, Fadda E, Agirre J.
Bagdonas H, et al.
Nat Struct Mol Biol. 2021 Nov;28(11):869-870. doi: 10.1038/s41594-021-00680-9.
Nat Struct Mol Biol. 2021.
PMID: 34716446
No abstract available.
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Leveraging glycomics data in glycoprotein 3D structure validation with Privateer.
Bagdonas H, Ungar D, Agirre J.
Bagdonas H, et al.
Beilstein J Org Chem. 2020 Oct 9;16:2523-2533. doi: 10.3762/bjoc.16.204. eCollection 2020.
Beilstein J Org Chem. 2020.
PMID: 33093930
Free PMC article.
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Structural glycobiology in the age of electron cryo-microscopy.
Atanasova M, Bagdonas H, Agirre J.
Atanasova M, et al. Among authors: bagdonas h.
Curr Opin Struct Biol. 2020 Jun;62:70-78. doi: 10.1016/j.sbi.2019.12.003. Epub 2019 Dec 23.
Curr Opin Struct Biol. 2020.
PMID: 31874387
Review.
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