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85 entries « 2 of 5 »
21.

Yakov Kipnis Brian D. Weitzner, A. Gerard Daniel

A computational method for design of connected catalytic networks in proteins Journal Article

In: Protein Science, 2019.

Abstract | Links | BibTeX

22.

Romero Romero, Maria Luisa; Yang, Fan; Lin, Yu-Ru; Toth-Petroczy, Agnes; Berezovsky, Igor N.; Goncearenco, Alexander; Yang, Wen; Wellner, Alon; Kumar-Deshmukh, Fanindra; Sharon, Michal; Baker, David; Varani, Gabriele; Tawfik, Dan S.

Simple yet functional phosphate-loop proteins Journal Article

In: PNAS, vol. 115, no. 51, pp. E11943–E11950, 2018, ISSN: 0027-8424.

Abstract | Links | BibTeX

23.

Yue-Ting K. Lau,; Vladimir Baytshtok,; Tessa A. Howard,; Brooke M. Fiala,; JayLee M. Johnson,; Lauren P. Carter,; David Baker,; Christopher D. Lima,; Bahl, Christopher D.

Discovery and engineering of enhanced SUMO protease enzymes Journal Article

In: The Journal of Biological Chemistry, vol. 293, pp. 13224-13233, 2018.

Abstract | Links | BibTeX

24.

Lu, Peilong; Min, Duyoung; DiMaio, Frank; Wei, Kathy Y.; Vahey, Michael D.; Boyken, Scott E.; Chen, Zibo; Fallas, Jorge A.; Ueda, George; Sheffler, William; Mulligan, Vikram Khipple; Xu, Wenqing; Bowie, James U.; Baker, David

Accurate computational design of multipass transmembrane proteins Journal Article

In: Science, vol. 359, no. 6379, pp. 1042–1046, 2018, ISSN: 0036-8075.

Abstract | Links | BibTeX

25.

Marcos, Enrique*; Basanta, Benjamin*; Chidyausiku, Tamuka M.; Tang, Yuefeng; Oberdorfer, Gustav; Liu, Gaohua; Swapna, G. V. T.; Guan, Rongjin; Silva, Daniel-Adriano; Dou, Jiayi; Pereira, Jose Henrique; Xiao, Rong; Sankaran, Banumathi; Zwart, Peter H.; Montelione, Gaetano T.; Baker, David

Principles for designing proteins with cavities formed by curved β sheets Journal Article

In: Science, vol. 355, no. 6321, pp. 201–206, 2017, ISSN: 0036-8075.

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26.

Bale, Jacob B.; Gonen, Shane; Liu, Yuxi; Sheffler, William; Ellis, Daniel; Thomas, Chantz; Cascio, Duilio; Yeates, Todd O.; Gonen, Tamir; King, Neil P.; Baker, David

Accurate design of megadalton-scale two-component icosahedral protein complexes Journal Article

In: Science, vol. 353, no. 6297, pp. 389-394, 2016.

Abstract | Links | BibTeX

27.

Doyle, L; Hallinan, J; Bolduc, J; Parmeggiani, F; Baker, D; Stoddard, BL; Bradley, P

Rational design of α-helical tandem repeat proteins with closed architectures Journal Article

In: Nature, vol. 528(7583), pp. 585-8, 2015.

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28.

Goldsmith, M; Eckstein, S; Ashani, Y; Greisen, P Jr; Leader, H; Sussman, JL; Aggarwal, N; Ovchinnikov, S; Tawfik, DS; Baker, D; Thiermann, H; Worek, F

Catalytic efficiencies of directly evolved phosphotriesterase variants with structurally different organophosphorus compounds in vitro Journal Article

In: Archives of Toxicology, 2015.

Abstract | Links | BibTeX

29.

Huang, PS; Feldmeier, K; Parmeggiani, F; Velasco, DA Fernandez; Höcker, B; Baker, D

De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy Journal Article

In: Nature Chemical Biology, vol. 12(1), pp. 29-34, 2015.

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30.

Wolf, Clancey; Siegel, Justin B; Tinberg, Christine; Camarca, Alessandra; Gianfrani, Carmen; Paski, Shirley; Guan, Rongjin; Montelione, Gaetano T; Baker, David; Pultz, Ingrid S

Engineering of Kuma030: a gliadin peptidase that rapidly degrades immunogenic gliadin peptides in gastric conditions. Journal Article

In: Journal of the American Chemical Society, 2015, ISSN: 1520-5126.

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31.

Siegel, Justin B; Smith, Amanda Lee; Poust, Sean; Wargacki, Adam J; Bar-Even, Arren; Louw, Catherine; Shen, Betty W; Eiben, Christopher B; Tran, Huu M; Noor, Elad; Gallaher, Jasmine L; Bale, Jacob; Yoshikuni, Yasuo; Gelb, Michael H; Keasling, Jay D; Stoddard, Barry L; Lidstrom, Mary E; Baker, David

Computational protein design enables a novel one-carbon assimilation pathway Journal Article

In: Proceedings of the National Academy of Sciences of the United States of America, 2015, ISSN: 1091-6490.

Abstract | Links | BibTeX

32.

Vittal, Vinayak; Shi, Lei; Wenzel, Dawn M; Scaglione, K Matthew; Duncan, Emily D; Basrur, Venkatesha; Elenitoba-Johnson, Kojo S J; Baker, David; Paulson, Henry L; Brzovic, Peter S; Klevit, Rachel E

Intrinsic disorder drives N-terminal ubiquitination by Ube2w Journal Article

In: Nature Chemical Biology, vol. 11, pp. 83-9, 2015, ISSN: 1552-4469.

Abstract | Links | BibTeX

33.

Liu, Daniel S; Niv’on, Lucas G; Richter, Florian; Goldman, Peter J; Deerinck, Thomas J; Yao, Jennifer Z; Richardson, Douglas; Phipps, William S; Ye, Anne Z; Ellisman, Mark H; Drennan, Catherine L; Baker, David; Ting, Alice Y

Computational design of a red fluorophore ligase for site-specific protein labeling in living cells. Journal Article

In: Proceedings of the National Academy of Sciences of the United States of America, vol. 111, pp. E4551-9, 2014, ISSN: 1091-6490.

Abstract | Links | BibTeX

34.

Liu, Yu; Zhang, Xin; Tan, Yun Lei; Bhabha, Gira; Ekiert, Damian C; Kipnis, Yakov; Bjelic, Sinisa; Baker, David; Kelly, Jeffery W

De novo-designed enzymes as small-molecule-regulated fluorescence imaging tags and fluorescent reporters. Journal Article

In: Journal of the American Chemical Society, vol. 136, pp. 13102-5, 2014, ISSN: 1520-5126.

Abstract | Links | BibTeX

35.

Preiswerk, Nathalie; Beck, Tobias; Schulz, Jessica D; Milovn’ik, Peter; Mayer, Clemens; Siegel, Justin B; Baker, David; Hilvert, Donald

Impact of scaffold rigidity on the design and evolution of an artificial Diels-Alderase. Journal Article

In: Proceedings of the National Academy of Sciences of the United States of America, vol. 111, pp. 8013-8, 2014, ISSN: 1091-6490.

Abstract | Links | BibTeX

36.

Ovchinnikov, Sergey; Kamisetty, Hetunandan; Baker, David

Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information. Journal Article

In: eLife, vol. 3, pp. e02030, 2014, ISSN: 2050-084X.

Abstract | Links | BibTeX

37.

Rajagopalan, Sridharan; Wang, Chu; Yu, Kai; Kuzin, Alexandre P; Richter, Florian; Lew, Scott; Miklos, Aleksandr E; Matthews, Megan L; Seetharaman, Jayaraman; Su, Min; Hunt, John F; Cravatt, Benjamin F; Baker, David

Design of activated serine-containing catalytic triads with atomic-level accuracy Journal Article

In: Nature chemical biology, vol. 10, pp. 386-391, 2014, ISSN: 1552-4469.

Abstract | Links | BibTeX

38.

Wang, Yupeng; Khan, Iram F; Boissel, Sandrine; Jarjour, Jordan; Pangallo, Joseph; Thyme, Summer; Baker, David; Scharenberg, Andrew M; Rawlings, David J

Progressive engineering of a homing endonuclease genome editing reagent for the murine X-linked immunodeficiency locus. Journal Article

In: Nucleic acids research, 2014, ISSN: 1362-4962.

Abstract | Links | BibTeX

39.

Liu, Yu; Tan, Yun Lei; Zhang, Xin; Bhabha, Gira; Ekiert, Damian C; Genereux, Joseph C; Cho, Younhee; Kipnis, Yakov; Bjelic, Sinisa; Baker, David; Kelly, Jeffery W

Small molecule probes to quantify the functional fraction of a specific protein in a cell with minimal folding equilibrium shifts. Journal Article

In: Proceedings of the National Academy of Sciences of the United States of America, 2014, ISSN: 1091-6490.

Abstract | Links | BibTeX

40.

Wijma, Hein J; Floor, Robert J; Jekel, Peter A; Baker, David; Marrink, Siewert J; Janssen, Dick B

Computationally designed libraries for rapid enzyme stabilization. Journal Article

In: Protein engineering, design & selection : PEDS, vol. 27, pp. 49-58, 2014, ISSN: 1741-0134.

Abstract | Links | BibTeX

85 entries « 2 of 5 »