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Approaches to ab initio molecular replacement of α-helical transmembrane proteins.
Thomas JMH, Simkovic F, Keegan R, Mayans O, Zhang C, Zhang Y, Rigden DJ. Thomas JMH, et al. Among authors: rigden dj. Acta Crystallogr D Struct Biol. 2017 Dec 1;73(Pt 12):985-996. doi: 10.1107/S2059798317016436. Epub 2017 Nov 22. Acta Crystallogr D Struct Biol. 2017. PMID: 29199978 Free PMC article.
Helical ensembles outperform ideal helices in molecular replacement.
Sánchez Rodríguez F, Simpkin AJ, Davies OR, Keegan RM, Rigden DJ. Sánchez Rodríguez F, et al. Among authors: rigden dj. Acta Crystallogr D Struct Biol. 2020 Oct 1;76(Pt 10):962-970. doi: 10.1107/S205979832001133X. Epub 2020 Sep 16. Acta Crystallogr D Struct Biol. 2020. PMID: 33021498 Free PMC article.
Evaluation of model refinement in CASP14.
Simpkin AJ, Sánchez Rodríguez F, Mesdaghi S, Kryshtafovych A, Rigden DJ. Simpkin AJ, et al. Among authors: rigden dj. Proteins. 2021 Dec;89(12):1852-1869. doi: 10.1002/prot.26185. Epub 2021 Jul 29. Proteins. 2021. PMID: 34288138 Free PMC article.
Multitasking in the gut: the X-ray structure of the multidomain BbgIII from Bifidobacterium bifidum offers possible explanations for its alternative functions.
Moroz OV, Blagova E, Lebedev AA, Sánchez Rodríguez F, Rigden DJ, Tams JW, Wilting R, Vester JK, Longhin E, Hansen GH, Krogh KBRM, Pache RA, Davies GJ, Wilson KS. Moroz OV, et al. Among authors: rigden dj. Acta Crystallogr D Struct Biol. 2021 Dec 1;77(Pt 12):1564-1578. doi: 10.1107/S2059798321010949. Epub 2021 Nov 17. Acta Crystallogr D Struct Biol. 2021. PMID: 34866612
Using deep-learning predictions of inter-residue distances for model validation.
Sánchez Rodríguez F, Chojnowski G, Keegan RM, Rigden DJ. Sánchez Rodríguez F, et al. Among authors: rigden dj. Acta Crystallogr D Struct Biol. 2022 Dec 1;78(Pt 12):1412-1427. doi: 10.1107/S2059798322010415. Epub 2022 Nov 25. Acta Crystallogr D Struct Biol. 2022. PMID: 36458613 Free PMC article.
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: rigden dj. 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.
Predicted models and CCP4.
Simpkin AJ, Caballero I, McNicholas S, Stevenson K, Jiménez E, Sánchez Rodríguez F, Fando M, Uski V, Ballard C, Chojnowski G, Lebedev A, Krissinel E, Usón I, Rigden DJ, Keegan RM. Simpkin AJ, et al. Among authors: rigden dj. Acta Crystallogr D Struct Biol. 2023 Sep 1;79(Pt 9):806-819. doi: 10.1107/S2059798323006289. Epub 2023 Aug 17. Acta Crystallogr D Struct Biol. 2023. PMID: 37594303 Free PMC article.
247 results