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Page 1
PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology.
Westbrook JD, Young JY, Shao C, Feng Z, Guranovic V, Lawson CL, Vallat B, Adams PD, Berrisford JM, Bricogne G, Diederichs K, Joosten RP, Keller P, Moriarty NW, Sobolev OV, Velankar S, Vonrhein C, Waterman DG, Kurisu G, Berman HM, Burley SK, Peisach E. Westbrook JD, et al. Among authors: joosten rp. J Mol Biol. 2022 Jun 15;434(11):167599. doi: 10.1016/j.jmb.2022.167599. Epub 2022 Apr 20. J Mol Biol. 2022. PMID: 35460671 Free PMC article. Review.
A new generation of crystallographic validation tools for the protein data bank.
Read RJ, Adams PD, Arendall WB 3rd, Brunger AT, Emsley P, Joosten RP, Kleywegt GJ, Krissinel EB, Lütteke T, Otwinowski Z, Perrakis A, Richardson JS, Sheffler WH, Smith JL, Tickle IJ, Vriend G, Zwart PH. Read RJ, et al. Among authors: joosten rp. Structure. 2011 Oct 12;19(10):1395-412. doi: 10.1016/j.str.2011.08.006. Structure. 2011. PMID: 22000512 Free PMC article.
New Biological Insights from Better Structure Models.
Touw WG, Joosten RP, Vriend G. Touw WG, et al. Among authors: joosten rp. J Mol Biol. 2016 Mar 27;428(6):1375-1393. doi: 10.1016/j.jmb.2016.02.002. Epub 2016 Feb 8. J Mol Biol. 2016. PMID: 26869101 Free article. Review.
Data Mining of Macromolecular Structures.
van Beusekom B, Perrakis A, Joosten RP. van Beusekom B, et al. Among authors: joosten rp. Methods Mol Biol. 2016;1415:107-38. doi: 10.1007/978-1-4939-3572-7_6. Methods Mol Biol. 2016. PMID: 27115630
West-Life: A Virtual Research Environment for structural biology.
Morris C, Andreetto P, Banci L, Bonvin AMJJ, Chojnowski G, Cano LD, Carazo JM, Conesa P, Daenke S, Damaskos G, Giachetti A, Haley NEC, Hekkelman ML, Heuser P, Joosten RP, Kouřil D, Křenek A, Kulhánek T, Lamzin VS, Nadzirin N, Perrakis A, Rosato A, Sanderson F, Segura J, Schaarschmidt J, Sobolev E, Traldi S, Trellet ME, Velankar S, Verlato M, Winn M. Morris C, et al. Among authors: joosten rp. J Struct Biol X. 2019 Feb 26;1:100006. doi: 10.1016/j.yjsbx.2019.100006. eCollection 2019 Jan-Mar. J Struct Biol X. 2019. PMID: 32647812 Free PMC article.
Modelling covalent linkages in CCP4.
Nicholls RA, Joosten RP, Long F, Wojdyr M, Lebedev A, Krissinel E, Catapano L, Fischer M, Emsley P, Murshudov GN. Nicholls RA, et al. Among authors: joosten rp. Acta Crystallogr D Struct Biol. 2021 Jun 1;77(Pt 6):712-726. doi: 10.1107/S2059798321001753. Epub 2021 May 19. Acta Crystallogr D Struct Biol. 2021. PMID: 34076587 Free PMC article.
New restraints and validation approaches for nucleic acid structures in PDB-REDO.
de Vries I, Kwakman T, Lu XJ, Hekkelman ML, Deshpande M, Velankar S, Perrakis A, Joosten RP. de Vries I, et al. Among authors: joosten rp. Acta Crystallogr D Struct Biol. 2021 Sep 1;77(Pt 9):1127-1141. doi: 10.1107/S2059798321007610. Epub 2021 Aug 24. Acta Crystallogr D Struct Biol. 2021. PMID: 34473084 Free PMC article.
3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources.
Varadi M, Nair S, Sillitoe I, Tauriello G, Anyango S, Bienert S, Borges C, Deshpande M, Green T, Hassabis D, Hatos A, Hegedus T, Hekkelman ML, Joosten R, Jumper J, Laydon A, Molodenskiy D, Piovesan D, Salladini E, Salzberg SL, Sommer MJ, Steinegger M, Suhajda E, Svergun D, Tenorio-Ku L, Tosatto S, Tunyasuvunakool K, Waterhouse AM, Žídek A, Schwede T, Orengo C, Velankar S. Varadi M, et al. Gigascience. 2022 Nov 30;11:giac118. doi: 10.1093/gigascience/giac118. Gigascience. 2022. PMID: 36448847 Free PMC article.
67 results