Publications

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1.

Hicks DR An L, Zorine D

Hallucination of closed repeat proteins containing central pockets Journal Article

In: Nature Structural & Molecular Biology, 2023.

Abstract | Links | BibTeX

2.

Wang, Jing Yang (John); Khmelinskaia, Alena; Sheffler, William; Miranda, Marcos C.; Antanasijevic, Aleksandar; Borst, Andrew J.; Torres, Susana V.; Shu, Chelsea; Hsia, Yang; Nattermann, Una; Ellis, Daniel; Walkey, Carl; Ahlrichs, Maggie; Chan, Sidney; Kang, Alex; Nguyen, Hannah; Sydeman, Claire; Sankaran, Banumathi; Wu, Mengyu; Bera, Asim K.; Carter, Lauren; Fiala, Brooke; Murphy, Michael; Baker, David; Ward, Andrew B.; King, Neil P.

Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains Journal Article

In: Proceedings of the National Academy of Sciences, 2023.

Abstract | Links | BibTeX

3.

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

4.

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

5.

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.

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6.

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.

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7.

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.

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8.

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.

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9.

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.

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10.

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

11.

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.

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12.

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

13.

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.

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14.

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