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.

Vulovic, Ivan; Yao, Qing; Park, Young-Jun; Courbet, Alexis; Norris, Andrew; Busch, Florian; Sahasrabuddhe, Aniruddha; Merten, Hannes; Sahtoe, Danny D.; Ueda, George; Fallas, Jorge A.; Weaver, Sara J.; Hsia, Yang; Langan, Robert A.; Pl"uckthun, Andreas; Wysocki, Vicki H.; Veesler, David; Jensen, Grant J.; Baker, David

Generation of ordered protein assemblies using rigid three-body fusion Journal Article

In: Proceedings of the National Academy of Sciences, vol. 118, no. 23, 2021.

Abstract | Links | BibTeX

3.

Hsia, Yang; Mout, Rubul; Sheffler, William; Edman, Natasha I.; Vulovic, Ivan; Park, Young-Jun; Redler, Rachel L.; Bick, Matthew J.; Bera, Asim K.; Courbet, Alexis; Kang, Alex; Brunette, T. J.; Nattermann, Una; Tsai, Evelyn; Saleem, Ayesha; Chow, Cameron M.; Ekiert, Damian; Bhabha, Gira; Veesler, David; Baker, David

Design of multi-scale protein complexes by hierarchical building block fusion Journal Article

In: Nature Communications, 2021.

Abstract | Links | BibTeX

4.

Ben-Sasson, Ariel J.; Watson, Joseph L.; Sheffler, William; Johnson, Matthew Camp; Bittleston, Alice; Somasundaram, Logeshwaran; Decarreau, Justin; Jiao, Fang; Chen, Jiajun; Mela, Ioanna; Drabek, Andrew A.; Jarrett, Sanchez M.; Blacklow, Stephen C.; Kaminski, Clemens F.; Hura, Greg L.; De Yoreo, James J.; Kollman, Justin M.; Ruohola-Baker, Hannele; Derivery, Emmanuel; Baker, David

Design of biologically active binary protein 2D materials Journal Article

In: Nature, 2021.

Abstract | Links | BibTeX

5.

Pyles, Harley; Zhang, Shuai; Yoreo, James J. De; Baker, David

Controlling protein assembly on inorganic crystals through designed protein interfaces Journal Article

In: Nature, 2019.

Abstract | Links | BibTeX

6.

Shen, Hao; Fallas, Jorge A.; Lynch, Eric; Sheffler, William; Parry, Bradley; Jannetty, Nicholas; Decarreau, Justin; Wagenbach, Michael; Vicente, Juan Jesus; Chen, Jiajun; Wang, Lei; Dowling, Quinton; Oberdorfer, Gustav; Stewart, Lance; Wordeman, Linda; De Yoreo, James; Jacobs-Wagner, Christine; Kollman, Justin; Baker, David

De novo design of self-assembling helical protein filaments Journal Article

In: Science, vol. 362, no. 6415, pp. 705–709, 2018, ISSN: 0036-8075.

Abstract | Links | BibTeX

7.

Butterfield, Gabriel L. *; Lajoie, Marc J. *; Gustafson, Heather H.; Sellers, Drew L.; Nattermann, Una; Ellis, Daniel; Bale, Jacob B.; Ke, Sharon; Lenz, Garreck H.; Yehdego, Angelica; Ravichandran, Rashmi; Pun, Suzie H.; King, Neil P.; Baker, David

Evolution of a designed protein assembly encapsulating its own RNA genome Journal Article

In: Nature, 2017, ISSN: 1476-4687.

Abstract | Links | BibTeX

8.

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

9.

Garcia, Kristen E; Babanova, Sofia; Scheffler, William; Hans, Mansij; Baker, David; Atanassov, Plamen; Banta, Scott

Designed protein aggregates entrapping carbon nanotubes for bioelectrochemical oxygen reduction Journal Article

In: Biotechnology and Bioengineering, pp. n/a–n/a, 2016, ISSN: 1097-0290.

Abstract | Links | BibTeX

10.

Boyken, Scott E.; Chen, Zibo; Groves, Benjamin; Langan, Robert A.; Oberdorfer, Gustav; Ford, Alex; Gilmore, Jason M.; Xu, Chunfu; DiMaio, Frank; Pereira, Jose Henrique; Sankaran, Banumathi; Seelig, Georg; Zwart, Peter H.; Baker, David

De novo design of protein homo-oligomers with modular hydrogen-bond network–mediated specificity Journal Article

In: Science, vol. 352, no. 6286, pp. 680–687, 2016, ISSN: 0036-8075.

Abstract | Links | BibTeX

11.

Doyle, L; Hallinan, J; Bolduc, J; Parmeggiani, F; Baker, D; Stoddard, BL; Bradley, P

Rational design of α-helical tandem repeat proteins with closed architectures Journal Article

In: Nature, vol. 528(7583), pp. 585-8, 2015.

Abstract | Links | BibTeX

12.

Bale, Jacob B; Park, Rachel U; Liu, Yuxi; Gonen, Shane; Gonen, Tamir; Cascio, Duilio; King, Neil P.; Yeates, Todd O.; Baker, David

Structure of a designed tetrahedral protein assembly variant engineered to have improved soluble expression Journal Article

In: Protein science : a publication of the Protein Society, 2015, ISSN: 1469-896X.

Abstract | Links | BibTeX

13.

Gonen, Shane; DiMaio, Frank; Gonen, Tamir; Baker, David

Design of ordered two-dimensional arrays mediated by noncovalent protein-protein interfaces Journal Article

In: Science (New York, N.Y.), vol. 348, pp. 1365-8, 2015, ISSN: 1095-9203.

Abstract | Links | BibTeX

14.

Parmeggiani, Fabio; Huang, Po-Ssu; Vorobiev, Sergey; Xiao, Rong; Park, Keunwan; Caprari, Silvia; Su, Min; Seetharaman, Jayaraman; Mao, Lei; Janjua, Haleema; Montelione, Gaetano T; Hunt, John; Baker, David

A General Computational Approach for Repeat Protein Design. Journal Article

In: Journal of molecular biology, 2014, ISSN: 1089-8638.

Abstract | Links | BibTeX

15.

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

16.

Fang, Jie; Mehlich, Alexander; Koga, Nobuyasu; Huang, Jiqing; Koga, Rie; Gao, Xiaoye; Hu, Chunguang; Jin, Chi; Rief, Matthias; Kast, Juergen; Baker, David; Li, Hongbin

Forced protein unfolding leads to highly elastic and tough protein hydrogels. Journal Article

In: Nature communications, vol. 4, pp. 2974, 2013, ISSN: 2041-1723.

Abstract | Links | BibTeX

17.

King, Neil P.; Sheffler, Will; Sawaya, Michael R; Vollmar, Breanna S.; Sumida, John P.; Andr'e, Ingemar; Gonen, Tamir; Yeates, Todd O.; Baker, David

Computational design of self-assembling protein nanomaterials with atomic level accuracy Journal Article

In: Science, 2012.

Abstract | Links | BibTeX

18.

Sadreyev, Ruslan I; Shi, ShuoYong; Baker, David; Grishin, Nick V

Structure similarity measure with penalty for close non-equivalent residues Journal Article

In: Bioinformatics, vol. 25, pp. 1259-63, 2009, ISSN: 1367-4811.

Abstract | BibTeX

 

2022

FROM THE LAB

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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

COLLABORATOR LED

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Sorry, no publications matched your criteria.

2021

FROM THE LAB

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Vulovic, Ivan, Yao, Qing, Park, Young-Jun, Courbet, Alexis, Norris, Andrew, Busch, Florian, Sahasrabuddhe, Aniruddha, Merten, Hannes, Sahtoe, Danny D., Ueda, George, Fallas, Jorge A., Weaver, Sara J., Hsia, Yang, Langan, Robert A., Pl"uckthun, Andreas, Wysocki, Vicki H., Veesler, David, Jensen, Grant J., Baker, David

Generation of ordered protein assemblies using rigid three-body fusion Journal Article

In: Proceedings of the National Academy of Sciences, vol. 118, no. 23, 2021.

Abstract | Links

Hsia, Yang and Mout, Rubul and Sheffler, William and Edman, Natasha I. and Vulovic, Ivan and Park, Young-Jun and Redler, Rachel L. and Bick, Matthew J. and Bera, Asim K. and Courbet, Alexis and Kang, Alex and Brunette, T. J. and Nattermann, Una and Tsai, Evelyn and Saleem, Ayesha and Chow, Cameron M. and Ekiert, Damian and Bhabha, Gira and Veesler, David and Baker, David

Design of multi-scale protein complexes by hierarchical building block fusion Journal Article

In: Nature Communications, 2021.

Abstract | Links

Ben-Sasson, Ariel J., Watson, Joseph L., Sheffler, William, Johnson, Matthew Camp, Bittleston, Alice, Somasundaram, Logeshwaran, Decarreau, Justin, Jiao, Fang, Chen, Jiajun, Mela, Ioanna, Drabek, Andrew A., Jarrett, Sanchez M., Blacklow, Stephen C., Kaminski, Clemens F., Hura, Greg L., De Yoreo, James J., Kollman, Justin M., Ruohola-Baker, Hannele, Derivery, Emmanuel, Baker, David

Design of biologically active binary protein 2D materials Journal Article

In: Nature, 2021.

Abstract | Links

COLLABORATOR LED

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Sorry, no publications matched your criteria.

2020

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.

2019

FROM THE LAB

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Harley Pyles, Shuai Zhang, James J. De Yoreo, David Baker

Controlling protein assembly on inorganic crystals through designed protein interfaces Journal Article

In: Nature, 2019.

Abstract | Links

COLLABORATOR LED

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Sorry, no publications matched your criteria.

2018

FROM THE LAB

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Shen, Hao, Fallas, Jorge A., Lynch, Eric, Sheffler, William, Parry, Bradley, Jannetty, Nicholas, Decarreau, Justin, Wagenbach, Michael, Vicente, Juan Jesus, Chen, Jiajun, Wang, Lei, Dowling, Quinton, Oberdorfer, Gustav, Stewart, Lance, Wordeman, Linda, De Yoreo, James, Jacobs-Wagner, Christine, Kollman, Justin, Baker, David

De novo design of self-assembling helical protein filaments Journal Article

In: Science, vol. 362, no. 6415, pp. 705–709, 2018, ISSN: 0036-8075.

Abstract | Links

COLLABORATOR LED

Show all

Sorry, no publications matched your criteria.

2017–1998

ALL PAPERS

Show all

2017

Butterfield, Gabriel L.* and Lajoie, Marc J.* and Gustafson, Heather H. and Sellers, Drew L. and Nattermann, Una and Ellis, Daniel and Bale, Jacob B. and Ke, Sharon and Lenz, Garreck H. and Yehdego, Angelica and Ravichandran, Rashmi and Pun, Suzie H. and King, Neil P. and Baker, David

Evolution of a designed protein assembly encapsulating its own RNA genome Journal Article

In: Nature, 2017, ISSN: 1476-4687.

Abstract | Links

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

Scott E. Boyken, Zibo Chen, Benjamin Groves, Robert A. Langan, Gustav Oberdorfer, Alex Ford, Jason M. Gilmore, Chunfu Xu, Frank DiMaio, Jose Henrique Pereira, Banumathi Sankaran, Georg Seelig, Peter H. Zwart, David Baker

De novo design of protein homo-oligomers with modular hydrogen-bond network–mediated specificity Journal Article

In: Science, vol. 352, no. 6286, pp. 680–687, 2016, ISSN: 0036-8075.

Abstract | Links

Kristen E Garcia, Sofia Babanova, William Scheffler, Mansij Hans, David Baker, Plamen Atanassov, Scott Banta

Designed protein aggregates entrapping carbon nanotubes for bioelectrochemical oxygen reduction Journal Article

In: Biotechnology and Bioengineering, pp. n/a–n/a, 2016, ISSN: 1097-0290.

Abstract | Links

2015

L Doyle, J Hallinan, J Bolduc, F Parmeggiani, D Baker, BL Stoddard, P Bradley

Rational design of α-helical tandem repeat proteins with closed architectures Journal Article

In: Nature, vol. 528(7583), pp. 585-8, 2015.

Abstract | Links

Jacob B Bale, Rachel U Park, Yuxi Liu, Shane Gonen, Tamir Gonen, Duilio Cascio, Neil P. King, Todd O. Yeates, David Baker

Structure of a designed tetrahedral protein assembly variant engineered to have improved soluble expression Journal Article

In: Protein science : a publication of the Protein Society, 2015, ISSN: 1469-896X.

Abstract | Links

Shane Gonen, Frank DiMaio, Tamir Gonen, David Baker

Design of ordered two-dimensional arrays mediated by noncovalent protein-protein interfaces Journal Article

In: Science (New York, N.Y.), vol. 348, pp. 1365-8, 2015, ISSN: 1095-9203.

Abstract | Links

2014

Fabio Parmeggiani, Po-Ssu Huang, Sergey Vorobiev, Rong Xiao, Keunwan Park, Silvia Caprari, Min Su, Jayaraman Seetharaman, Lei Mao, Haleema Janjua, Gaetano T Montelione, John Hunt, David Baker

A General Computational Approach for Repeat Protein Design. Journal Article

In: Journal of molecular biology, 2014, ISSN: 1089-8638.

Abstract | Links

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

Jie Fang, Alexander Mehlich, Nobuyasu Koga, Jiqing Huang, Rie Koga, Xiaoye Gao, Chunguang Hu, Chi Jin, Matthias Rief, Juergen Kast, David Baker, Hongbin Li

Forced protein unfolding leads to highly elastic and tough protein hydrogels. Journal Article

In: Nature communications, vol. 4, pp. 2974, 2013, ISSN: 2041-1723.

Abstract | Links

2012

Neil P. King, Will Sheffler, Michael R Sawaya, Breanna S. Vollmar, John P. Sumida, Ingemar Andr'e, Tamir Gonen, Todd O. Yeates, David Baker

Computational design of self-assembling protein nanomaterials with atomic level accuracy Journal Article

In: Science, 2012.

Abstract | Links

2009

Ruslan I Sadreyev, ShuoYong Shi, David Baker, Nick V Grishin

Structure similarity measure with penalty for close non-equivalent residues Journal Article

In: Bioinformatics, vol. 25, pp. 1259-63, 2009, ISSN: 1367-4811.

Abstract