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Page 1
Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge.
Lawson CL, Kryshtafovych A, Pintilie GD, Burley SK, Černý J, Chen VB, Emsley P, Gobbi A, Joachimiak A, Noreng S, Prisant MG, Read RJ, Richardson JS, Rohou AL, Schneider B, Sellers BD, Shao C, Sourial E, Williams CI, Williams CJ, Yang Y, Abbaraju V, Afonine PV, Baker ML, Bond PS, Blundell TL, Burnley T, Campbell A, Cao R, Cheng J, Chojnowski G, Cowtan KD, DiMaio F, Esmaeeli R, Giri N, Grubmüller H, Hoh SW, Hou J, Hryc CF, Hunte C, Igaev M, Joseph AP, Kao WC, Kihara D, Kumar D, Lang L, Lin S, Maddhuri Venkata Subramaniya SR, Mittal S, Mondal A, Moriarty NW, Muenks A, Murshudov GN, Nicholls RA, Olek M, Palmer CM, Perez A, Pohjolainen E, Pothula KR, Rowley CN, Sarkar D, Schäfer LU, Schlicksup CJ, Schröder GF, Shekhar M, Si D, Singharoy A, Sobolev OV, Terashi G, Vaiana AC, Vedithi SC, Verburgt J, Wang X, Warshamanage R, Winn MD, Weyand S, Yamashita K, Zhao M, Schmid MF, Berman HM, Chiu W. Lawson CL, et al. Among authors: sobolev ov. Nat Methods. 2024 Jul;21(7):1340-1348. doi: 10.1038/s41592-024-02321-7. Epub 2024 Jun 25. Nat Methods. 2024. PMID: 38918604 Free PMC article.
FEM: feature-enhanced map.
Afonine PV, Moriarty NW, Mustyakimov M, Sobolev OV, Terwilliger TC, Turk D, Urzhumtsev A, Adams PD. Afonine PV, et al. Among authors: sobolev ov. Acta Crystallogr D Biol Crystallogr. 2015 Mar;71(Pt 3):646-66. doi: 10.1107/S1399004714028132. Epub 2015 Feb 26. Acta Crystallogr D Biol Crystallogr. 2015. PMID: 25760612 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. Among authors: sobolev ov. 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.
Real-space quantum-based refinement for cryo-EM: Q|R#3.
Wang L, Kruse H, Sobolev OV, Moriarty NW, Waller MP, Afonine PV, Biczysko M. Wang L, et al. Among authors: sobolev ov. Acta Crystallogr D Struct Biol. 2020 Dec 1;76(Pt 12):1184-1191. doi: 10.1107/S2059798320013194. Epub 2020 Nov 19. Acta Crystallogr D Struct Biol. 2020. PMID: 33263324
Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge.
Lawson CL, Kryshtafovych A, Pintilie GD, Burley SK, Černý J, Chen VB, Emsley P, Gobbi A, Joachimiak A, Noreng S, Prisant M, Read RJ, Richardson JS, Rohou AL, Schneider B, Sellers BD, Shao C, Sourial E, Williams CI, Williams CJ, Yang Y, Abbaraju V, Afonine PV, Baker ML, Bond PS, Blundell TL, Burnley T, Campbell A, Cao R, Cheng J, Chojnowski G, Cowtan KD, DiMaio F, Esmaeeli R, Giri N, Grubmüller H, Hoh SW, Hou J, Hryc CF, Hunte C, Igaev M, Joseph AP, Kao WC, Kihara D, Kumar D, Lang L, Lin S, Maddhuri Venkata Subramaniya SR, Mittal S, Mondal A, Moriarty NW, Muenks A, Murshudov GN, Nicholls RA, Olek M, Palmer CM, Perez A, Pohjolainen E, Pothula KR, Rowley CN, Sarkar D, Schäfer LU, Schlicksup CJ, Schröder GF, Shekhar M, Si D, Singharoy A, Sobolev OV, Terashi G, Vaiana AC, Vedithi SC, Verburgt J, Wang X, Warshamanage R, Winn MD, Weyand S, Yamashita K, Zhao M, Schmid MF, Berman HM, Chiu W. Lawson CL, et al. Among authors: sobolev ov. Res Sq [Preprint]. 2024 Jan 25:rs.3.rs-3864137. doi: 10.21203/rs.3.rs-3864137/v1. Res Sq. 2024. Update in: Nat Methods. 2024 Jul;21(7):1340-1348. doi: 10.1038/s41592-024-02321-7 PMID: 38343795 Free PMC article. Updated. Preprint.
Density modification of cryo-EM maps.
Terwilliger TC, Sobolev OV, Afonine PV, Adams PD, Read RJ. Terwilliger TC, et al. Among authors: sobolev ov. Acta Crystallogr D Struct Biol. 2020 Oct 1;76(Pt 10):912-925. doi: 10.1107/S205979832001061X. Epub 2020 Sep 22. Acta Crystallogr D Struct Biol. 2020. PMID: 33021493 Free PMC article.
Overall protein structure quality assessment using hydrogen-bonding parameters.
Afonine PV, Sobolev OV, Moriarty NW, Terwilliger TC, Adams PD. Afonine PV, et al. Among authors: sobolev ov. Acta Crystallogr D Struct Biol. 2023 Aug 1;79(Pt 8):684-693. doi: 10.1107/S2059798323005077. Epub 2023 Jul 11. Acta Crystallogr D Struct Biol. 2023. PMID: 37431759 Free PMC article.
Cryo_fit: Democratization of flexible fitting for cryo-EM.
Kim DN, Moriarty NW, Kirmizialtin S, Afonine PV, Poon B, Sobolev OV, Adams PD, Sanbonmatsu K. Kim DN, et al. Among authors: sobolev ov. J Struct Biol. 2019 Oct 1;208(1):1-6. doi: 10.1016/j.jsb.2019.05.012. Epub 2019 Jul 3. J Struct Biol. 2019. PMID: 31279069 Free PMC article.
Real-space refinement in PHENIX for cryo-EM and crystallography.
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. Afonine PV, et al. Among authors: sobolev ov. Acta Crystallogr D Struct Biol. 2018 Jun 1;74(Pt 6):531-544. doi: 10.1107/S2059798318006551. Epub 2018 May 30. Acta Crystallogr D Struct Biol. 2018. PMID: 29872004 Free PMC article.
24 results