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Page 1
Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank.
Burley SK, Bhatt R, Bhikadiya C, Bi C, Biester A, Biswas P, Bittrich S, Blaumann S, Brown R, Chao H, Chithari VR, Craig PA, Crichlow GV, Duarte JM, Dutta S, Feng Z, Flatt JW, Ghosh S, Goodsell DS, Green RK, Guranovic V, Henry J, Hudson BP, Joy M, Kaelber JT, Khokhriakov I, Lai JS, Lawson CL, Liang Y, Myers-Turnbull D, Peisach E, Persikova I, Piehl DW, Pingale A, Rose Y, Sagendorf J, Sali A, Segura J, Sekharan M, Shao C, Smith J, Trumbull M, Vallat B, Voigt M, Webb B, Whetstone S, Wu-Wu A, Xing T, Young JY, Zalevsky A, Zardecki C. Burley SK, et al. Among authors: zalevsky a. Nucleic Acids Res. 2024 Nov 28:gkae1091. doi: 10.1093/nar/gkae1091. Online ahead of print. Nucleic Acids Res. 2024. PMID: 39607707
Illuminating the function of the orphan transporter, SLC22A10, in humans and other primates.
Yee SW, Ferrández-Peral L, Alentorn-Moron P, Fontsere C, Ceylan M, Koleske ML, Handin N, Artegoitia VM, Lara G, Chien HC, Zhou X, Dainat J, Zalevsky A, Sali A, Brand CM, Wolfreys FD, Yang J, Gestwicki JE, Capra JA, Artursson P, Newman JW, Marquès-Bonet T, Giacomini KM. Yee SW, et al. Among authors: zalevsky a. Nat Commun. 2024 May 23;15(1):4380. doi: 10.1038/s41467-024-48569-7. Nat Commun. 2024. PMID: 38782905 Free PMC article.
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. Among authors: zalevsky a. J Mol Biol. 2024 Sep 1;436(17):168546. doi: 10.1016/j.jmb.2024.168546. Epub 2024 Mar 18. J Mol Biol. 2024. PMID: 38508301 Free PMC article.
Structures, functions and adaptations of the human LINE-1 ORF2 protein.
Baldwin ET, van Eeuwen T, Hoyos D, Zalevsky A, Tchesnokov EP, Sánchez R, Miller BD, Di Stefano LH, Ruiz FX, Hancock M, Işik E, Mendez-Dorantes C, Walpole T, Nichols C, Wan P, Riento K, Halls-Kass R, Augustin M, Lammens A, Jestel A, Upla P, Xibinaku K, Congreve S, Hennink M, Rogala KB, Schneider AM, Fairman JE, Christensen SM, Desrosiers B, Bisacchi GS, Saunders OL, Hafeez N, Miao W, Kapeller R, Zaller DM, Sali A, Weichenrieder O, Burns KH, Götte M, Rout MP, Arnold E, Greenbaum BD, Romero DL, LaCava J, Taylor MS. Baldwin ET, et al. Among authors: zalevsky a. Nature. 2024 Feb;626(7997):194-206. doi: 10.1038/s41586-023-06947-z. Epub 2023 Dec 14. Nature. 2024. PMID: 38096902 Free PMC article.
Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates.
Yee SW, Ferrández-Peral L, Alentorn P, Fontsere C, Ceylan M, Koleske ML, Handin N, Artegoitia VM, Lara G, Chien HC, Zhou X, Dainat J, Zalevsky A, Sali A, Brand CM, Capra JA, Artursson P, Newman JW, Marques-Bonet T, Giacomini KM. Yee SW, et al. Among authors: zalevsky a. Res Sq [Preprint]. 2023 Sep 14:rs.3.rs-3263845. doi: 10.21203/rs.3.rs-3263845/v1. Res Sq. 2023. Update in: Nat Commun. 2024 May 23;15(1):4380. doi: 10.1038/s41467-024-48569-7 PMID: 37790518 Free PMC article. Updated. Preprint.
Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates.
Yee SW, Ferrández-Peral L, Alentorn P, Fontsere C, Ceylan M, Koleske ML, Handin N, Artegoitia VM, Lara G, Chien HC, Zhou X, Dainat J, Zalevsky A, Sali A, Brand CM, Capra JA, Artursson P, Newman JW, Marques-Bonet T, Giacomini KM. Yee SW, et al. Among authors: zalevsky a. bioRxiv [Preprint]. 2023 Aug 12:2023.08.08.552553. doi: 10.1101/2023.08.08.552553. bioRxiv. 2023. Update in: Nat Commun. 2024 May 23;15(1):4380. doi: 10.1038/s41467-024-48569-7 PMID: 37609337 Free PMC article. Updated. Preprint.
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. Among authors: zalevsky a. Nucleic Acids Res. 2023 Jan 6;51(D1):D488-D508. doi: 10.1093/nar/gkac1077. Nucleic Acids Res. 2023. PMID: 36420884 Free PMC article.
A structural biology community assessment of AlphaFold2 applications.
Akdel M, Pires DEV, Pardo EP, Jänes J, Zalevsky AO, Mészáros B, Bryant P, Good LL, Laskowski RA, Pozzati G, Shenoy A, Zhu W, Kundrotas P, Serra VR, Rodrigues CHM, Dunham AS, Burke D, Borkakoti N, Velankar S, Frost A, Basquin J, Lindorff-Larsen K, Bateman A, Kajava AV, Valencia A, Ovchinnikov S, Durairaj J, Ascher DB, Thornton JM, Davey NE, Stein A, Elofsson A, Croll TI, Beltrao P. Akdel M, et al. Among authors: zalevsky ao. Nat Struct Mol Biol. 2022 Nov;29(11):1056-1067. doi: 10.1038/s41594-022-00849-w. Epub 2022 Nov 7. Nat Struct Mol Biol. 2022. PMID: 36344848 Free PMC article.
RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D.
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 SJ, 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. Among authors: zalevsky a. Protein Sci. 2022 Dec;31(12):e4482. doi: 10.1002/pro.4482. Protein Sci. 2022. PMID: 36281733 Free PMC article.
37 results