Publications

Preprints are available on bioRxiv.

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1.

Wicky, B. I. M.; Milles, L. F.; Courbet, A.; Ragotte, R. J.; Dauparas, J.; Kinfu, E.; Tipps, S.; Kibler, R. D.; Baek, M.; DiMaio, F.; Li, X.; Carter, L.; Kang, A.; Nguyen, H.; Bera, A. K.; Baker, D.

Hallucinating symmetric protein assemblies Journal Article

In: Science, 2022.

Abstract | Links | BibTeX

2.

Courbet, A.; Hansen, J.; Hsia, Y.; Bethel, N.; Park, Y. -J.; Xu, C.; Moyer, A.; Boyken, S. E.; Ueda, G.; Nattermann, U.; Nagarajan, D.; Silva, D.; Sheffler, W.; Quispe, J.; Nord, A.; King, N.; Bradley, P.; Veesler, D.; Kollman, J.; Baker, D.

Computational design of mechanically coupled axle-rotor protein assemblies Journal Article

In: Science, 2022.

Abstract | Links | BibTeX

3.

Linder, Johannes; La Fleur, Alyssa; Chen, Zibo; Ljubetič, Ajasja; Baker, David; Kannan, Sreeram; Seelig, Georg

Interpreting neural networks for biological sequences by learning stochastic masks Journal Article

In: Nature Machine Intelligence, 2022.

Abstract | Links | BibTeX

4.

Yaman, Muammer Y; Guye, Kathryn N; Ziatdinov, Maxim; Shen, Hao; Baker, David; Kalinin, Sergei V; Ginger, David S

Alignment of Au nanorods along de novo designed protein nanofibers studied with automated image analysis Journal Article

In: Soft Matter, 2021.

Abstract | Links | BibTeX

5.

Vorobieva, Anastassia A.; White, Paul; Liang, Binyong; Horne, Jim E.; Bera, Asim K.; Chow, Cameron M.; Gerben, Stacey; Marx, Sinduja; Kang, Alex; Stiving, Alyssa Q.; Harvey, Sophie R.; Marx, Dagan C.; Khan, G. Nasir; Fleming, Karen G.; Wysocki, Vicki H.; Brockwell, David J.; Tamm, Lukas K.; Radford, Sheena E.; Baker, David

De novo design of transmembrane beta barrels Journal Article

In: Science, vol. 371, no. 6531, 2021.

Abstract | Links | BibTeX

6.

Chen, Zibo; Kibler, Ryan D.; Hunt, Andrew; Busch, Florian; Pearl, Jocelynn; Jia, Mengxuan; VanAernum, Zachary L.; Wicky, Basile I. M.; Dods, Galen; Liao, Hanna; Wilken, Matthew S.; Ciarlo, Christie; Green, Shon; El-Samad, Hana; Stamatoyannopoulos, John; Wysocki, Vicki H.; Jewett, Michael C.; Boyken, Scott E.; Baker, David

De novo design of protein logic gates Journal Article

In: Science, vol. 368, no. 6486, pp. 78-84, 2020.

Abstract | Links | BibTeX

7.

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

8.

King, Neil P.; Bale, Jacob B; Sheffler, William; McNamara, Dan E; Gonen, Shane; Gonen, Tamir; Yeates, Todd O.; Baker, David

Accurate design of co-assembling multi-component protein nanomaterials. Journal Article

In: Nature, 2014, ISSN: 1476-4687.

Abstract | Links | BibTeX

9.

Demers, Jean-Philippe; Sgourakis, Nikolaos G; Gupta, Rashmi; Loquet, Antoine; Giller, Karin; Riedel, Dietmar; Laube, Britta; Kolbe, Michael; Baker, David; Becker, Stefan; Lange, Adam

The common structural architecture of Shigella flexneri and Salmonella typhimurium type three secretion needles Journal Article

In: PLoS pathogens, vol. 9, pp. e1003245, 2013, ISSN: 1553-7374.

Abstract | Links | BibTeX

10.

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

11.

Warner, Lisa R; Varga, Krisztina; Lange, Oliver F; Baker, Susan L; Baker, David; Sousa, Marcelo C; Pardi, Arthur

Structure of the BamC two-domain protein obtained by Rosetta with a limited NMR data set Journal Article

In: Journal of Molecular Biology, vol. 411, pp. 83-95, 2011, ISSN: 1089-8638.

Abstract | Links | BibTeX

12.

Zhang, Junjie; Ma, Boxue; DiMaio, Frank; Douglas, Nicholai R; Joachimiak, Lukasz A; Baker, David; Frydman, Judith; Levitt, Michael; Chiu, Wah

Cryo-EM structure of a group II chaperonin in the prehydrolysis ATP-bound state leading to lid closure Journal Article

In: Structure (London, England : 1993), vol. 19, pp. 633-9, 2011, ISSN: 1878-4186.

Abstract | Links | BibTeX

13.

Sanowar, Sarah; Singh, Pragya; Pfuetzner, Richard A; Andr'e, Ingemar; Zheng, Hongjin; Spreter, Thomas; Strynadka, Natalie C J; Gonen, Tamir; Baker, David; Goodlett, David R; Miller, Samuel I

Interactions of the Transmembrane Polymeric Rings of the Salmonella enterica Serovar Typhimurium Type III Secretion System Journal Article

In: mBio, vol. 1, 2010, ISSN: 2150-7511.

Abstract | BibTeX

14.

S, Raman; B, Qian; D, Baker; RC, Walker

Advances in Rosetta Protein Structure Prediction on Massively Parallel Systems Journal Article

In: Journal of Research and Development, vol. 52(1-2):7-17, 2008.

Abstract | BibTeX

15.

Dantas, Gautam; Watters, Alexander L; Lunde, Bradley M; Eletr, Ziad M; Isern, Nancy G; Roseman, Toby; Lipfert, Jan; Doniach, Sebastian; Tompa, Martin; Kuhlman, Brian; Stoddard, Barry L; Varani, Gabriele; Baker, David

Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution Journal Article

In: Journal of molecular biology, vol. 362, pp. 1004-24, 2006, ISSN: 0022-2836.

Abstract | Links | BibTeX

 

2022

FROM THE LAB

Show all

B. I. M. Wicky, L. F. Milles, A. Courbet, R. J. Ragotte, J. Dauparas, E. Kinfu, S. Tipps, R. D. Kibler, M. Baek, F. DiMaio, X. Li, L. Carter, A. Kang, H. Nguyen, A. K. Bera, D. Baker

Hallucinating symmetric protein assemblies Journal Article

In: Science, 2022.

Abstract | Links

A. Courbet, J. Hansen, Y. Hsia, N. Bethel, Y.-J. Park, C. Xu, A. Moyer, S. E. Boyken, G. Ueda, U. Nattermann, D. Nagarajan, D. Silva, W. Sheffler, J. Quispe, A. Nord, N. King, P. Bradley, D. Veesler, J. Kollman, D. Baker

Computational design of mechanically coupled axle-rotor protein assemblies Journal Article

In: Science, 2022.

Abstract | Links

COLLABORATOR LED

Show all

Linder, Johannes, La Fleur, Alyssa, Chen, Zibo, Ljubetič, Ajasja, Baker, David, Kannan, Sreeram, Seelig, Georg

Interpreting neural networks for biological sequences by learning stochastic masks Journal Article

In: Nature Machine Intelligence, 2022.

Abstract | Links

2021

FROM THE LAB

Show all

Vorobieva, Anastassia A., White, Paul, Liang, Binyong, Horne, Jim E., Bera, Asim K., Chow, Cameron M., Gerben, Stacey, Marx, Sinduja, Kang, Alex, Stiving, Alyssa Q., Harvey, Sophie R., Marx, Dagan C., Khan, G. Nasir, Fleming, Karen G., Wysocki, Vicki H., Brockwell, David J., Tamm, Lukas K., Radford, Sheena E., Baker, David

De novo design of transmembrane beta barrels Journal Article

In: Science, vol. 371, no. 6531, 2021.

Abstract | Links

COLLABORATOR LED

Show all

Muammer Y Yaman, Kathryn N Guye, Maxim Ziatdinov, Hao Shen, David Baker, Sergei V Kalinin, David S Ginger

Alignment of Au nanorods along de novo designed protein nanofibers studied with automated image analysis Journal Article

In: Soft Matter, 2021.

Abstract | Links

2020

FROM THE LAB

Show all

Chen, Zibo, Kibler, Ryan D., Hunt, Andrew, Busch, Florian, Pearl, Jocelynn, Jia, Mengxuan, VanAernum, Zachary L., Wicky, Basile I. M., Dods, Galen, Liao, Hanna, Wilken, Matthew S., Ciarlo, Christie, Green, Shon, El-Samad, Hana, Stamatoyannopoulos, John, Wysocki, Vicki H., Jewett, Michael C., Boyken, Scott E., Baker, David

De novo design of protein logic gates Journal Article

In: Science, vol. 368, no. 6486, pp. 78-84, 2020.

Abstract | Links

COLLABORATOR LED

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Sorry, no publications matched your criteria.

2019

FROM THE LAB

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Sorry, no publications matched your criteria.

COLLABORATOR LED

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Sorry, no publications matched your criteria.

2018

FROM THE LAB

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Sorry, no publications matched your criteria.

COLLABORATOR LED

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Sorry, no publications matched your criteria.

2017–1998

ALL PAPERS

Show all

2016

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

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

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

Abstract | Links

2014

Neil P. King, Jacob B Bale, William Sheffler, Dan E McNamara, Shane Gonen, Tamir Gonen, Todd O. Yeates, David Baker

Accurate design of co-assembling multi-component protein nanomaterials. Journal Article

In: Nature, 2014, ISSN: 1476-4687.

Abstract | Links

2013

Jean-Philippe Demers, Nikolaos G Sgourakis, Rashmi Gupta, Antoine Loquet, Karin Giller, Dietmar Riedel, Britta Laube, Michael Kolbe, David Baker, Stefan Becker, Adam Lange

The common structural architecture of Shigella flexneri and Salmonella typhimurium type three secretion needles Journal Article

In: PLoS pathogens, vol. 9, pp. e1003245, 2013, ISSN: 1553-7374.

Abstract | Links

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

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

2011

Lisa R Warner, Krisztina Varga, Oliver F Lange, Susan L Baker, David Baker, Marcelo C Sousa, Arthur Pardi

Structure of the BamC two-domain protein obtained by Rosetta with a limited NMR data set Journal Article

In: Journal of Molecular Biology, vol. 411, pp. 83-95, 2011, ISSN: 1089-8638.

Abstract | Links

Junjie Zhang, Boxue Ma, Frank DiMaio, Nicholai R Douglas, Lukasz A Joachimiak, David Baker, Judith Frydman, Michael Levitt, Wah Chiu

Cryo-EM structure of a group II chaperonin in the prehydrolysis ATP-bound state leading to lid closure Journal Article

In: Structure (London, England : 1993), vol. 19, pp. 633-9, 2011, ISSN: 1878-4186.

Abstract | Links

2010

Sarah Sanowar, Pragya Singh, Richard A Pfuetzner, Ingemar Andr'e, Hongjin Zheng, Thomas Spreter, Natalie C J Strynadka, Tamir Gonen, David Baker, David R Goodlett, Samuel I Miller

Interactions of the Transmembrane Polymeric Rings of the Salmonella enterica Serovar Typhimurium Type III Secretion System Journal Article

In: mBio, vol. 1, 2010, ISSN: 2150-7511.

Abstract

2008

Raman S, Qian B, Baker D, Walker RC

Advances in Rosetta Protein Structure Prediction on Massively Parallel Systems Journal Article

In: Journal of Research and Development, vol. 52(1-2):7-17, 2008.

Abstract

2006

Gautam Dantas, Alexander L Watters, Bradley M Lunde, Ziad M Eletr, Nancy G Isern, Toby Roseman, Jan Lipfert, Sebastian Doniach, Martin Tompa, Brian Kuhlman, Barry L Stoddard, Gabriele Varani, David Baker

Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution Journal Article

In: Journal of molecular biology, vol. 362, pp. 1004-24, 2006, ISSN: 0022-2836.

Abstract | Links