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Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks.
Koehler Leman J, Lyskov S, Lewis SM, Adolf-Bryfogle J, Alford RF, Barlow K, Ben-Aharon Z, Farrell D, Fell J, Hansen WA, Harmalkar A, Jeliazkov J, Kuenze G, Krys JD, Ljubetič A, Loshbaugh AL, Maguire J, Moretti R, Mulligan VK, Nance ML, Nguyen PT, Ó Conchúir S, Roy Burman SS, Samanta R, Smith ST, Teets F, Tiemann JKS, Watkins A, Woods H, Yachnin BJ, Bahl CD, Bailey-Kellogg C, Baker D, Das R, DiMaio F, Khare SD, Kortemme T, Labonte JW, Lindorff-Larsen K, Meiler J, Schief W, Schueler-Furman O, Siegel JB, Stein A, Yarov-Yarovoy V, Kuhlman B, Leaver-Fay A, Gront D, Gray JJ, Bonneau R. Koehler Leman J, et al. Among authors: farrell d. Nat Commun. 2021 Nov 29;12(1):6947. doi: 10.1038/s41467-021-27222-7. Nat Commun. 2021. PMID: 34845212 Free PMC article.
Structural basis for autophagy inhibition by the human Rubicon-Rab7 complex.
Bhargava HK, Tabata K, Byck JM, Hamasaki M, Farrell DP, Anishchenko I, DiMaio F, Im YJ, Yoshimori T, Hurley JH. Bhargava HK, et al. Proc Natl Acad Sci U S A. 2020 Jul 21;117(29):17003-17010. doi: 10.1073/pnas.2008030117. Epub 2020 Jul 6. Proc Natl Acad Sci U S A. 2020. PMID: 32632011 Free PMC article.
Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge.
Lawson CL, Kryshtafovych A, Adams PD, Afonine PV, Baker ML, Barad BA, Bond P, Burnley T, Cao R, Cheng J, Chojnowski G, Cowtan K, Dill KA, DiMaio F, Farrell DP, Fraser JS, Herzik MA Jr, Hoh SW, Hou J, Hung LW, Igaev M, Joseph AP, Kihara D, Kumar D, Mittal S, Monastyrskyy B, Olek M, Palmer CM, Patwardhan A, Perez A, Pfab J, Pintilie GD, Richardson JS, Rosenthal PB, Sarkar D, Schäfer LU, Schmid MF, Schröder GF, Shekhar M, Si D, Singharoy A, Terashi G, Terwilliger TC, Vaiana A, Wang L, Wang Z, Wankowicz SA, Williams CJ, Winn M, Wu T, Yu X, Zhang K, Berman HM, Chiu W. Lawson CL, et al. Among authors: farrell dp. Nat Methods. 2021 Feb;18(2):156-164. doi: 10.1038/s41592-020-01051-w. Epub 2021 Feb 4. Nat Methods. 2021. PMID: 33542514 Free PMC article.
BRCA1/BARD1 site-specific ubiquitylation of nucleosomal H2A is directed by BARD1.
Witus SR, Burrell AL, Farrell DP, Kang J, Wang M, Hansen JM, Pravat A, Tuttle LM, Stewart MD, Brzovic PS, Chatterjee C, Zhao W, DiMaio F, Kollman JM, Klevit RE. Witus SR, et al. Among authors: farrell dp. Nat Struct Mol Biol. 2021 Mar;28(3):268-277. doi: 10.1038/s41594-020-00556-4. Epub 2021 Feb 15. Nat Struct Mol Biol. 2021. PMID: 33589814 Free PMC article.
851 results