Publications

Preprints are available on bioRxiv.

Show all

78 entries « 3 of 4 »
41.

Kiss, Gert; c"um, Nihan Celebi-"Olc; Moretti, Rocco; Baker, David; Houk, K N

Computational enzyme design Journal Article

In: Angewandte Chemie (International ed. in English), vol. 52, pp. 5700-25, 2013, ISSN: 1521-3773.

Abstract | Links | BibTeX

42.

Harger, Matthew; Zheng, Lei; Moon, Austin; Ager, Casey; An, Ju Hye; Choe, Chris; Lai, Yi-Ling; Mo, Benjamin; Zong, David; Smith, Matthew D; Egbert, Robert G; Mills, Jeremy H; Baker, David; Pultz, Ingrid Swanson; Siegel, Justin B

Expanding the product profile of a microbial alkane biosynthetic pathway. Journal Article

In: ACS synthetic biology, vol. 2, pp. 59-62, 2013, ISSN: 2161-5063.

Abstract | Links | BibTeX

43.

Niv'on, Lucas Gregorio; Moretti, Rocco; Baker, David

A Pareto-optimal refinement method for protein design scaffolds Journal Article

In: PloS one, vol. 8, pp. e59004, 2013, ISSN: 1932-6203.

Abstract | Links | BibTeX

44.

Gordon, Sydney R; Stanley, Elizabeth J; Wolf, Sarah; Toland, Angus; Wu, Sean J; Hadidi, Daniel; Mills, Jeremy H; Baker, David; Pultz, Ingrid Swanson; Siegel, Justin B

Computational Design of an α-gliadin Peptidase Journal Article

In: Journal of the American Chemical Society, vol. 134, pp. 20513-20, 2012, ISSN: 1520-5126.

Abstract | Links | BibTeX

45.

Richter, Florian; Blomberg, Rebecca; Khare, Sagar D; Kiss, Gert; Kuzin, Alexandre P; Smith, Adam J T; Gallaher, Jasmine; Pianowski, Zbigniew; Helgeson, Roger C; Grjasnow, Alexej; Xiao, Rong; Seetharaman, Jayaraman; Su, Min; Vorobiev, Sergey; Lew, Scott; Forouhar, Farhad; Kornhaber, Gregory J; Hunt, John F; Montelione, Gaetano T; Tong, Liang; Houk, K N; Hilvert, Donald; Baker, David

Computational design of catalytic dyads and oxyanion holes for ester hydrolysis. Journal Article

In: Journal of the American Chemical Society, vol. 134, pp. 16197-206, 2012, ISSN: 1520-5126.

Abstract | Links | BibTeX

46.

Kipnis, Yakov; Baker, David

Comparison of designed and randomly generated catalysts for simple chemical reactions Journal Article

In: Protein Science : A Publication of the Protein Society, vol. 21, pp. 1388-95, 2012, ISSN: 1469-896X.

Abstract | Links | BibTeX

47.

Baxter, Sarah; Lambert, Abigail R; Kuhar, Ryan; Jarjour, Jordan; Kulshina, Nadia; Parmeggiani, Fabio; Danaher, Patrick; Gano, Jacob; Baker, David; Stoddard, Barry L; Scharenberg, Andrew M

Engineering domain fusion chimeras from I-OnuI family LAGLIDADG homing endonucleases. Journal Article

In: Nucleic acids research, vol. 40, pp. 7985-8000, 2012, ISSN: 1362-4962.

Abstract | Links | BibTeX

48.

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

The dynamic disulphide relay of quiescin sulphydryl oxidase Journal Article

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

Abstract | Links | BibTeX

49.

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

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 | BibTeX

50.

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

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 | BibTeX

51.

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

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

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

Abstract | Links | BibTeX

52.

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

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 | BibTeX

53.

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

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 | BibTeX

54.

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

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 | BibTeX

55.

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

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 | BibTeX

56.

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

De Novo Enzyme Design Using Rosetta3 Journal Article

In: PLoS, 2011.

Abstract | Links | BibTeX

57.

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

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 | BibTeX

58.

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

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 | BibTeX

59.

Liu, Lingfeng; Murphy, Paul; Baker, David; Lutz, Stefan

Computational design of orthogonal nucleoside kinases Journal Article

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

Abstract | BibTeX

60.

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

Evaluation and ranking of enzyme designs Journal Article

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

Abstract | Links | BibTeX

78 entries « 3 of 4 »

 

2022

FROM THE LAB

Show all

Sorry, no publications matched your criteria.

COLLABORATOR LED

Show all

Sorry, no publications matched your criteria.

2021

FROM THE LAB

Show all

Sorry, no publications matched your criteria.

COLLABORATOR LED

Show all

Sorry, no publications matched your criteria.

2020

FROM THE LAB

Show all

Sorry, no publications matched your criteria.

COLLABORATOR LED

Show all

Sorry, no publications matched your criteria.

2019

FROM THE LAB

Show all

Sorry, no publications matched your criteria.

COLLABORATOR LED

Show all

Sorry, no publications matched your criteria.

2018

FROM THE LAB

Show all

Sorry, no publications matched your criteria.

COLLABORATOR LED

Show all

Sorry, no publications matched your criteria.

2017–1998

ALL PAPERS

Show all

61 entries « 3 of 3 »

1992

D Baker, J L Silen, D A Agard

Protease pro region required for folding is a potent inhibitor of the mature enzyme Journal Article

In: Proteins, vol. 12, pp. 339-44, 1992, ISSN: 0887-3585.

Abstract

61 entries « 3 of 3 »