Publications

Preprints are available on bioRxiv.

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1.

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

2.

Xu, Chunfu; Lu, Peilong; El-Din, Tamer M. Gamal; Pei, Xue Y.; Johnson, Matthew C.; Uyeda, Atsuko; Bick, Matthew J.; Xu, Qi; Jiang, Daohua; Bai, Hua; Reggiano, Gabriella; Hsia, Yang; Brunette, T J; Dou, Jiayi; Ma, Dan; Lynch, Eric M.; Boyken, Scott E.; Huang, Po-Ssu; Stewart, Lance; DiMaio, Frank; Kollman, Justin M.; Luisi, Ben F.; Matsuura, Tomoaki; Catterall, William A.; Baker, David

Computational design of transmembrane pores Journal Article

In: Nature, vol. 585, pp. 129–134, 2020.

Abstract | Links | BibTeX

3.

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

4.

Bergeron, Julien R C; Worrall, Liam J; De, Soumya; Sgourakis, Nikolaos G; Cheung, Adrienne H; Lameignere, Emilie; Okon, Mark; Wasney, Gregory A; Baker, David; McIntosh, Lawrence P; Strynadka, Natalie C J

The modular structure of the inner-membrane ring component PrgK facilitates assembly of the type III secretion system basal body Journal Article

In: Structure (London, England : 1993), vol. 23, pp. 161-72, 2015, ISSN: 1878-4186.

Abstract | Links | BibTeX

5.

Chen, Kuang-Yui M; Sun, Jiaming; Salvo, Jason S; Baker, David; Barth, Patrick

High-resolution modeling of transmembrane helical protein structures from distant homologues. Journal Article

In: PLoS computational biology, vol. 10, pp. e1003636, 2014, ISSN: 1553-7358.

Abstract | Links | BibTeX

6.

Yarov-Yarovoy, Vladimir; DeCaen, Paul G; Westenbroek, Ruth E; Pan, Chien-Yuan; Scheuer, Todd; Baker, David; Catterall, William A

Structural basis for gating charge movement in the voltage sensor of a sodium channel Journal Article

In: Proceedings of the National Academy of Sciences of the United States of America, vol. 109, pp. E93-102, 2012, ISSN: 1091-6490.

Abstract | Links | BibTeX

7.

Saha, Piyali; Barua, Bipasha; Bhattacharyya, Sanchari; Balamurali, M M; Schief, William R; Baker, David; Varadarajan, Raghavan

Design and characterization of stabilized derivatives of human CD4D12 and CD4D1 Journal Article

In: Biochemistry, vol. 50, pp. 7891-900, 2011, ISSN: 1520-4995.

Abstract | Links | BibTeX

8.

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

9.

Zhu, Jieqing; Luo, Bing-Hao; Barth, Patrick; Schonbrun, Jack; Baker, David; Springer, Timothy A

The structure of a receptor with two associating transmembrane domains on the cell surface: integrin alphaIIbbeta3 Journal Article

In: Molecular cell, vol. 34, pp. 234-49, 2009, ISSN: 1097-4164.

Abstract | BibTeX

10.

Luo, Bing-Hao; Karanicolas, John; Harmacek, Laura D; Baker, David; Springer, Timothy A

Rationally designed integrin beta3 mutants stabilized in the high affinity conformation Journal Article

In: The Journal of biological chemistry, vol. 284, pp. 3917-24, 2009, ISSN: 0021-9258.

Abstract | BibTeX

11.

Barth, P; Schonbrun, J; Baker, David

Toward high-resolution prediction and design of transmembrane helical protein structures Journal Article

In: Proceedings of the National Academy of Sciences of the United States of America, vol. 104, pp. 15682-7, 2007, ISSN: 0027-8424.

Abstract | Links | BibTeX

12.

Yarov-Yarovoy, Vladimir; Schonbrun, Jack; Baker, David

Multipass membrane protein structure prediction using Rosetta Journal Article

In: Proteins, vol. 62, pp. 1010-25, 2006, ISSN: 1097-0134.

Abstract | Links | BibTeX

 

2022

FROM THE LAB

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COLLABORATOR LED

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2021

FROM THE LAB

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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

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Sorry, no publications matched your criteria.

2020

FROM THE LAB

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Chunfu Xu, Peilong Lu, Tamer M. Gamal El-Din, Xue Y. Pei, Matthew C. Johnson, Atsuko Uyeda, Matthew J. Bick, Qi Xu, Daohua Jiang, Hua Bai, Gabriella Reggiano, Yang Hsia, T J Brunette, Jiayi Dou, Dan Ma, Eric M. Lynch, Scott E. Boyken, Po-Ssu Huang, Lance Stewart, Frank DiMaio, Justin M. Kollman, Ben F. Luisi, Tomoaki Matsuura, William A. Catterall, David Baker

Computational design of transmembrane pores Journal Article

In: Nature, vol. 585, pp. 129–134, 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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2018

FROM THE LAB

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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

COLLABORATOR LED

Show all

Sorry, no publications matched your criteria.

2017–1998

ALL PAPERS

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2015

Julien R C Bergeron, Liam J Worrall, Soumya De, Nikolaos G Sgourakis, Adrienne H Cheung, Emilie Lameignere, Mark Okon, Gregory A Wasney, David Baker, Lawrence P McIntosh, Natalie C J Strynadka

The modular structure of the inner-membrane ring component PrgK facilitates assembly of the type III secretion system basal body Journal Article

In: Structure (London, England : 1993), vol. 23, pp. 161-72, 2015, ISSN: 1878-4186.

Abstract | Links

2014

Kuang-Yui M Chen, Jiaming Sun, Jason S Salvo, David Baker, Patrick Barth

High-resolution modeling of transmembrane helical protein structures from distant homologues. Journal Article

In: PLoS computational biology, vol. 10, pp. e1003636, 2014, ISSN: 1553-7358.

Abstract | Links

2012

Vladimir Yarov-Yarovoy, Paul G DeCaen, Ruth E Westenbroek, Chien-Yuan Pan, Todd Scheuer, David Baker, William A Catterall

Structural basis for gating charge movement in the voltage sensor of a sodium channel Journal Article

In: Proceedings of the National Academy of Sciences of the United States of America, vol. 109, pp. E93-102, 2012, ISSN: 1091-6490.

Abstract | Links

2011

Piyali Saha, Bipasha Barua, Sanchari Bhattacharyya, M M Balamurali, William R Schief, David Baker, Raghavan Varadarajan

Design and characterization of stabilized derivatives of human CD4D12 and CD4D1 Journal Article

In: Biochemistry, vol. 50, pp. 7891-900, 2011, ISSN: 1520-4995.

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

2009

Jieqing Zhu, Bing-Hao Luo, Patrick Barth, Jack Schonbrun, David Baker, Timothy A Springer

The structure of a receptor with two associating transmembrane domains on the cell surface: integrin alphaIIbbeta3 Journal Article

In: Molecular cell, vol. 34, pp. 234-49, 2009, ISSN: 1097-4164.

Abstract

Bing-Hao Luo, John Karanicolas, Laura D Harmacek, David Baker, Timothy A Springer

Rationally designed integrin beta3 mutants stabilized in the high affinity conformation Journal Article

In: The Journal of biological chemistry, vol. 284, pp. 3917-24, 2009, ISSN: 0021-9258.

Abstract

2007

P Barth, J Schonbrun, David Baker

Toward high-resolution prediction and design of transmembrane helical protein structures Journal Article

In: Proceedings of the National Academy of Sciences of the United States of America, vol. 104, pp. 15682-7, 2007, ISSN: 0027-8424.

Abstract | Links

2006

Vladimir Yarov-Yarovoy, Jack Schonbrun, David Baker

Multipass membrane protein structure prediction using Rosetta Journal Article

In: Proteins, vol. 62, pp. 1010-25, 2006, ISSN: 1097-0134.

Abstract | Links