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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: afonine pv. Res Sq [Preprint]. 2024 Jan 25:rs.3.rs-3864137. doi: 10.21203/rs.3.rs-3864137/v1. Res Sq. 2024. PMID: 38343795 Free PMC article. Preprint.
Improved joint X-ray and neutron refinement procedure in Phenix.
Liebschner D, Afonine PV, Poon BK, Moriarty NW, Adams PD. Liebschner D, et al. Among authors: afonine pv. Acta Crystallogr D Struct Biol. 2023 Dec 1;79(Pt 12):1079-1093. doi: 10.1107/S2059798323008914. Epub 2023 Nov 9. Acta Crystallogr D Struct Biol. 2023. PMID: 37942718 Free PMC article.
Accelerating crystal structure determination with iterative AlphaFold prediction.
Terwilliger TC, Afonine PV, Liebschner D, Croll TI, McCoy AJ, Oeffner RD, Williams CJ, Poon BK, Richardson JS, Read RJ, Adams PD. Terwilliger TC, et al. Among authors: afonine pv. Acta Crystallogr D Struct Biol. 2023 Mar 1;79(Pt 3):234-244. doi: 10.1107/S205979832300102X. Epub 2023 Feb 27. Acta Crystallogr D Struct Biol. 2023. PMID: 36876433 Free PMC article.
Improved AlphaFold modeling with implicit experimental information.
Terwilliger TC, Poon BK, Afonine PV, Schlicksup CJ, Croll TI, Millán C, Richardson JS, Read RJ, Adams PD. Terwilliger TC, et al. Among authors: afonine pv. Nat Methods. 2022 Nov;19(11):1376-1382. doi: 10.1038/s41592-022-01645-6. Epub 2022 Oct 20. Nat Methods. 2022. PMID: 36266465 Free PMC article.
92 results