Publications

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78 entries « 2 of 4 »
21.

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

22.

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.

Abstract | Links | BibTeX

23.

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.

Abstract | Links | BibTeX

24.

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

25.

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

26.

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

27.

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

28.

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

29.

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

30.

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

31.

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

32.

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

33.

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

34.

Thyme, Summer; Baker, David

Redesigning the Specificity of Protein-DNA Interactions with Rosetta. Journal Article

In: Methods in molecular biology (Clifton, N.J.), vol. 1123, pp. 265-82, 2014, ISSN: 1940-6029.

Abstract | Links | BibTeX

35.

Shropshire, Tyler D; Reifert, Jack; Rajagopalan, Sridharan; Baker, David; Feinstein, Stuart C; Daugherty, Patrick S

Amyloid β peptide cleavage by kallikrein 7 attenuates fibril growth and rescues neurons from Aβ-mediated toxicity in vitro. Journal Article

In: Biological chemistry, vol. 395, pp. 109-18, 2014, ISSN: 1437-4315.

Abstract | Links | BibTeX

36.

Cherny, Izhack; Greisen, Per; Ashani, Yacov; Khare, Sagar D; Oberdorfer, Gustav; Leader, Haim; Baker, David; Tawfik, Dan S

Engineering V-type nerve agents detoxifying enzymes using computationally focused libraries Journal Article

In: ACS chemical biology, vol. 8, pp. 2394-403, 2013, ISSN: 1554-8937.

Abstract | Links | BibTeX

37.

Niv'on, Lucas G; Bjelic, Sinisa; King, Chris; Baker, David

Automating human intuition for protein design Journal Article

In: Proteins, 2013, ISSN: 1097-0134.

Abstract | Links | BibTeX

38.

Mills, Jeremy H; Khare, Sagar D; Bolduc, Jill M; Forouhar, Farhad; Mulligan, Vikram Khipple; Lew, Scott; Seetharaman, Jayaraman; Tong, Liang; Stoddard, Barry L; Baker, David

Computational design of an unnatural amino acid dependent metalloprotein with atomic level accuracy. Journal Article

In: Journal of the American Chemical Society, vol. 135, pp. 13393-9, 2013, ISSN: 1520-5126.

Abstract | Links | BibTeX

39.

Procko, Erik; Hedman, Rickard; Hamilton, Keith; Seetharaman, Jayaraman; Fleishman, Sarel J; Su, Min; Aramini, James; Kornhaber, Gregory; Hunt, John F; Tong, Liang; Montelione, Gaetano T; Baker, David

Computational design of a protein-based enzyme inhibitor. Journal Article

In: Journal of molecular biology, vol. 425, pp. 3563-75, 2013, ISSN: 1089-8638.

Abstract | Links | BibTeX

40.

Giger, Lars; Caner, Sami; Obexer, Richard; Kast, Peter; Baker, David; Ban, Nenad; Hilvert, Donald

Evolution of a designed retro-aldolase leads to complete active site remodeling. Journal Article

In: Nature chemical biology, vol. 9, pp. 494-8, 2013, ISSN: 1552-4469.

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78 entries « 2 of 4 »

 

2022

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2021

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2020

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2019

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2018

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2017–1998

ALL PAPERS

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61 entries « 2 of 3 »

2012

Assaf Alon, Iris Grossman, Yair Gat, Vamsi K Kodali, Frank DiMaio, Tevie Mehlman, Gilad Haran, David Baker, Colin Thorpe, Deborah Fass

The dynamic disulphide relay of quiescin sulphydryl oxidase Journal Article

In: Nature, vol. 488, pp. 414-8, 2012, ISSN: 1476-4687.

Abstract | Links

Olga Khersonsky, Gert Kiss, Daniela R"othlisberger, Orly Dym, Shira Albeck, Kendall N Houk, David Baker, Dan S Tawfik

Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59. Journal Article

In: Proceedings of the National Academy of Sciences of the United States of America, vol. 109, pp. 10358-63, 2012, ISSN: 1091-6490.

Abstract | Links

Eric A Althoff, Ling Wang, Lin Jiang, Lars Giger, Jonathan K Lassila, Zhizhi Wang, Matthew Smith, Sanjay Hari, Peter Kast, Daniel Herschlag, Donald Hilvert, David Baker

Robust design and optimization of retroaldol enzymes. Journal Article

In: Protein science : a publication of the Protein Society, vol. 21, pp. 717-26, 2012, ISSN: 1469-896X.

Abstract | Links

Sagar D Khare, Yakov Kipnis, Per Jr Greisen, Ryo Takeuchi, Yacov Ashani, Moshe Goldsmith, Yifan Song, Jasmine L Gallaher, Israel Silman, Haim Leader, Joel L Sussman, Barry L Stoddard, Dan S Tawfik, David Baker

Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis Journal Article

In: Nature chemical biology, 2012, ISSN: 1552-4469.

Abstract | Links

Adam J Wargacki, Effendi Leonard, Maung Nyan Win, Drew D Regitsky, Christine Nicole S Santos, Peter B Kim, Susan R Cooper, Ryan M Raisner, Asael Herman, Alicia B Sivitz, Arun Lakshmanaswamy, Yuki Kashiyama, David Baker, Yasuo Yoshikuni

An engineered microbial platform for direct biofuel production from brown macroalgae Journal Article

In: Science, vol. 335, pp. 308-13, 2012, ISSN: 1095-9203.

Abstract | Links

Ling Wang, Eric A Althoff, Jill Bolduc, Lin Jiang, James Moody, Jonathan K Lassila, Lars Giger, Donald Hilvert, Barry Stoddard, David Baker

Structural analyses of covalent enzyme-substrate analog complexes reveal strengths and limitations of de novo enzyme design Journal Article

In: Journal of molecular biology, vol. 415, pp. 615-25, 2012, ISSN: 1089-8638.

Abstract | Links

Christopher B Eiben, Justin B Siegel, Jacob B Bale, Seth Cooper, Firas Khatib, Betty W Shen, Foldit Players, Barry L Stoddard, Zoran Popovic, David Baker

Increased Diels-Alderase activity through backbone remodeling guided by Foldit players Journal Article

In: Nature biotechnology, vol. 30, pp. 190-2, 2012, ISSN: 1546-1696.

Abstract | Links

2011

Mindy D Szeto, Sandrine J S Boissel, David Baker, Summer B Thyme

Mining endonuclease cleavage determinants in genomic sequence data. Journal Article

In: The Journal of biological chemistry, vol. 286, pp. 32617-27, 2011, ISSN: 1083-351X.

Abstract | Links

Richter, Florian AND Leaver-Fay, Andrew AND Khare, Sagar D. AND Bjelic, Sinisa AND Baker, David

De Novo Enzyme Design Using Rosetta3 Journal Article

In: PLoS, 2011.

Abstract | Links

Olga Khersonsky, Daniela R"othlisberger, Andrew M Wollacott, Paul Murphy, Orly Dym, Shira Albeck, Gert Kiss, K N Houk, David Baker, Dan S Tawfik

Optimization of the In-Silico-Designed Kemp Eliminase KE70 by Computational Design and Directed Evolution Journal Article

In: Journal of molecular biology, vol. 407, pp. 391-412, 2011, ISSN: 1089-8638.

Abstract

Mi Li, Frank DiMaio, Dongwen Zhou, Alla Gustchina, Jacek Lubkowski, Zbigniew Dauter, David Baker, Alexander Wlodawer

Crystal structure of XMRV protease differs from the structures of other retropepsins Journal Article

In: Nature structural & molecular biology, vol. 18, pp. 227-9, 2011, ISSN: 1545-9985.

Abstract

2010

Lingfeng Liu, Paul Murphy, David Baker, Stefan Lutz

Computational design of orthogonal nucleoside kinases Journal Article

In: Chemical communications, vol. 46, pp. 8803-5, 2010, ISSN: 1364-548X.

Abstract

Gert Kiss, Daniela R"othlisberger, David Baker, K N Houk

Evaluation and ranking of enzyme designs Journal Article

In: Protein science, vol. 19, pp. 1760-73, 2010, ISSN: 1469-896X.

Abstract | Links

David Baker

An exciting but challenging road ahead for computational enzyme design Journal Article

In: Protein science, 2010, ISSN: 1469-896X.

Justin B Siegel, Alexandre Zanghellini, Helena M Lovick, Gert Kiss, Abigail R Lambert, Jennifer L St Clair, Jasmine L Gallaher, Donald Hilvert, Michael H Gelb, Barry L Stoddard, Kendall N Houk, Forrest E Michael, David Baker

Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction Journal Article

In: Science, vol. 329, pp. 309-13, 2010, ISSN: 1095-9203.

Abstract

Olga Khersonsky, Daniela R"othlisberger, Orly Dym, Shira Albeck, Colin J Jackson, David Baker, Dan S Tawfik

Evolutionary optimization of computationally designed enzymes: Kemp eliminases of the KE07 series Journal Article

In: Journal of Molecular Biology, vol. 396, pp. 1025-42, 2010, ISSN: 1089-8638.

Abstract | Links

2009

Summer B Thyme, Jordan Jarjour, Ryo Takeuchi, James J Havranek, Justin Ashworth, Andrew M Scharenberg, Barry L Stoddard, David Baker

Exploitation of binding energy for catalysis and design Journal Article

In: Nature, vol. 461, pp. 1300-4, 2009, ISSN: 1476-4687.

Abstract

Paul M Murphy, Jill M Bolduc, Jasmine L Gallaher, Barry L Stoddard, David Baker

Alteration of enzyme specificity by computational loop remodeling and design Journal Article

In: Proceedings of the National Academy of Sciences of the United States of America, vol. 106, pp. 9215-20, 2009, ISSN: 1091-6490.

Abstract

Kathryn E Muratore, Markus A Seeliger, Zhihong Wang, Dina Fomina, Johnathan Neiswinger, James J Havranek, David Baker, John Kuriyan, Philip A Cole

Comparative analysis of mutant tyrosine kinase chemical rescue Journal Article

In: Biochemistry, vol. 48, pp. 3378-86, 2009, ISSN: 1520-4995.

Abstract

Jeffrey A Dietrich, Yasuo Yoshikuni, Karl J Fisher, Frank X Woolard, Denise Ockey, Derek J McPhee, Neil S Renninger, Michelle C Y Chang, David Baker, Jay D Keasling

A novel semi-biosynthetic route for artemisinin production using engineered substrate-promiscuous P450(BM3) Journal Article

In: ACS chemical biology, vol. 4, pp. 261-7, 2009, ISSN: 1554-8937.

Abstract

2008

Anastassia N Alexandrova, Daniela R"othlisberger, David Baker, William L Jorgensen

Catalytic mechanism and performance of computationally designed enzymes for Kemp elimination Journal Article

In: Journal of the American Chemical Society, vol. 130, pp. 15907-15, 2008, ISSN: 1520-5126.

Abstract

Hyundae D Cho, Vanita D Sood, David Baker, Alan M Weiner

On the role of a conserved, potentially helix-breaking residue in the tRNA-binding alpha-helix of archaeal CCA-adding enzymes Journal Article

In: RNA, vol. 14, pp. 1284-9, 2008, ISSN: 1469-9001.

Abstract

Daniela R"othlisberger, Olga Khersonsky, Andrew M Wollacott, Lin Jiang, Jason DeChancie, Jamie Betker, Jasmine L Gallaher, Eric A Althoff, Alexandre Zanghellini, Orly Dym, Shira Albeck, Kendall N Houk, Dan S Tawfik, David Baker

Kemp elimination catalysts by computational enzyme design Journal Article

In: Nature, vol. 453, pp. 190-5, 2008, ISSN: 1476-4687.

Abstract

Lin Jiang, Eric A Althoff, Fernando R Clemente, Lindsey Doyle, Daniela R"othlisberger, Alexandre Zanghellini, Jasmine L Gallaher, Jamie L Betker, Fujie Tanaka, Carlos F Barbas, Donald Hilvert, Kendall N Houk, Barry L Stoddard, David Baker

De novo computational design of retro-aldol enzymes Journal Article

In: Science, vol. 319, pp. 1387-91, 2008, ISSN: 1095-9203.

Abstract

2006

Alexandre Zanghellini, Lin Jiang, Andrew M Wollacott, Gong Cheng, Jens Meiler, Eric A Althoff, Daniela R"othlisberger, David Baker

New algorithms and an in silico benchmark for computational enzyme design Journal Article

In: Protein science : a publication of the Protein Society, vol. 15, pp. 2785-94, 2006, ISSN: 0961-8368.

Abstract | Links

Justin Ashworth, James J Havranek, Carlos M Duarte, Django Sussman, Raymond J Monnat, Barry L Stoddard, David Baker

Computational redesign of endonuclease DNA binding and cleavage specificity Journal Article

In: Nature, vol. 441, pp. 656-9, 2006, ISSN: 1476-4687.

Abstract | Links

2005

D Borden Lacy, Henry C Lin, Roman A Melnyk, Ora Schueler-Furman, Laura Reither, Kristina Cunningham, David Baker, R John Collier

A model of anthrax toxin lethal factor bound to protective antigen Journal Article

In: Proceedings of the National Academy of Sciences of the United States of America, vol. 102, pp. 16409-14, 2005, ISSN: 0027-8424.

Abstract | Links

Aaron Korkegian, Margaret E Black, David Baker, Barry L Stoddard

Computational thermostabilization of an enzyme Journal Article

In: Science, vol. 308, pp. 857-60, 2005, ISSN: 1095-9203.

Abstract | Links

2002

Brett S Chevalier, Tanja Kortemme, Meggen S Chadsey, David Baker, Raymond J Monnat, Barry L Stoddard

Design, activity, and structure of a highly specific artificial endonuclease Journal Article

In: Molecular cell, vol. 10, pp. 895-905, 2002, ISSN: 1097-2765.

Abstract | Links

1993

D Baker, A K Shiau, D A Agard

The role of pro regions in protein folding. Journal Article

In: Current Opinion in Cell Biology, vol. 5, pp. 966-70, 1993, ISSN: 0955-0674.

Abstract | Links

61 entries « 2 of 3 »