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RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning.
Burley SK, Bhikadiya C, Bi C, Bittrich S, Chao H, Chen L, Craig PA, Crichlow GV, Dalenberg K, Duarte JM, Dutta S, Fayazi M, Feng Z, Flatt JW, Ganesan S, Ghosh S, Goodsell DS, Green RK, Guranovic V, Henry J, Hudson BP, Khokhriakov I, Lawson CL, Liang Y, Lowe R, Peisach E, Persikova I, Piehl DW, Rose Y, Sali A, Segura J, Sekharan M, Shao C, Vallat B, Voigt M, Webb B, Westbrook JD, Whetstone S, Young JY, Zalevsky A, Zardecki C. Burley SK, et al. Nucleic Acids Res. 2023 Jan 6;51(D1):D488-D508. doi: 10.1093/nar/gkac1077. Nucleic Acids Res. 2023. PMID: 36420884 Free PMC article.
Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures.
Berman HM, Adams PD, Bonvin AA, Burley SK, Carragher B, Chiu W, DiMaio F, Ferrin TE, Gabanyi MJ, Goddard TD, Griffin PR, Haas J, Hanke CA, Hoch JC, Hummer G, Kurisu G, Lawson CL, Leitner A, Markley JL, Meiler J, Montelione GT, Phillips GN Jr, Prisner T, Rappsilber J, Schriemer DC, Schwede T, Seidel CAM, Strutzenberg TS, Svergun DI, Tajkhorshid E, Trewhella J, Vallat B, Velankar S, Vuister GW, Webb B, Westbrook JD, White KL, Sali A. Berman HM, et al. Structure. 2019 Dec 3;27(12):1745-1759. doi: 10.1016/j.str.2019.11.002. Epub 2019 Nov 25. Structure. 2019. PMID: 31780431 Free PMC article.
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. 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.
Archiving of Integrative Structural Models.
Berman HM, Trewhella J, Vallat B, Westbrook JD. Berman HM, et al. Adv Exp Med Biol. 2018;1105:261-272. doi: 10.1007/978-981-13-2200-6_16. Adv Exp Med Biol. 2018. PMID: 30617834 Review.
IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods.
Vallat B, Webb BM, Westbrook JD, Goddard TD, Hanke CA, Graziadei A, Peisach E, Zalevsky A, Sagendorf J, Tangmunarunkit H, Voinea S, Sekharan M, Yu J, Bonvin AAMJJ, DiMaio F, Hummer G, Meiler J, Tajkhorshid E, Ferrin TE, Lawson CL, Leitner A, Rappsilber J, Seidel CAM, Jeffries CM, Burley SK, Hoch JC, Kurisu G, Morris K, Patwardhan A, Velankar S, Schwede T, Trewhella J, Kesselman C, Berman HM, Sali A. Vallat B, et al. J Mol Biol. 2024 Mar 18:168546. doi: 10.1016/j.jmb.2024.168546. Online ahead of print. J Mol Biol. 2024. PMID: 38508301 Free article.
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