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The dynamic conformational landscape of the protein methyltransferase SETD8.
Chen S, Wiewiora RP, Meng F, Babault N, Ma A, Yu W, Qian K, Hu H, Zou H, Wang J, Fan S, Blum G, Pittella-Silva F, Beauchamp KA, Tempel W, Jiang H, Chen K, Skene RJ, Zheng YG, Brown PJ, Jin J, Luo C, Chodera JD, Luo M. Chen S, et al. Among authors: beauchamp ka. Elife. 2019 May 13;8:e45403. doi: 10.7554/eLife.45403. Elife. 2019. PMID: 31081496 Free PMC article.
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics.
Eastman P, Swails J, Chodera JD, McGibbon RT, Zhao Y, Beauchamp KA, Wang LP, Simmonett AC, Harrigan MP, Stern CD, Wiewiora RP, Brooks BR, Pande VS. Eastman P, et al. Among authors: beauchamp ka. PLoS Comput Biol. 2017 Jul 26;13(7):e1005659. doi: 10.1371/journal.pcbi.1005659. eCollection 2017 Jul. PLoS Comput Biol. 2017. PMID: 28746339 Free PMC article.
Escaping Atom Types in Force Fields Using Direct Chemical Perception.
Mobley DL, Bannan CC, Rizzi A, Bayly CI, Chodera JD, Lim VT, Lim NM, Beauchamp KA, Slochower DR, Shirts MR, Gilson MK, Eastman PK. Mobley DL, et al. Among authors: beauchamp ka. J Chem Theory Comput. 2018 Nov 13;14(11):6076-6092. doi: 10.1021/acs.jctc.8b00640. Epub 2018 Oct 30. J Chem Theory Comput. 2018. PMID: 30351006 Free PMC article.
MSMBuilder: Statistical Models for Biomolecular Dynamics.
Harrigan MP, Sultan MM, Hernández CX, Husic BE, Eastman P, Schwantes CR, Beauchamp KA, McGibbon RT, Pande VS. Harrigan MP, et al. Among authors: beauchamp ka. Biophys J. 2017 Jan 10;112(1):10-15. doi: 10.1016/j.bpj.2016.10.042. Biophys J. 2017. PMID: 28076801 Free PMC article.
From a structural average to the conformational ensemble of a DNA bulge.
Shi X, Beauchamp KA, Harbury PB, Herschlag D. Shi X, et al. Among authors: beauchamp ka. Proc Natl Acad Sci U S A. 2014 Apr 15;111(15):E1473-80. doi: 10.1073/pnas.1317032111. Epub 2014 Mar 31. Proc Natl Acad Sci U S A. 2014. PMID: 24706812 Free PMC article.
46 results