Publications

Preprints are available on bioRxiv.

Show all

77 entries « 1 of 4 »
1.

Wang, Jue; Lisanza, Sidney; Juergens, David; Tischer, Doug; Watson, Joseph L.; Castro, Karla M.; Ragotte, Robert; Saragovi, Amijai; Milles, Lukas F.; Baek, Minkyung; Anishchenko, Ivan; Yang, Wei; Hicks, Derrick R.; Expòsit, Marc; Schlichthaerle, Thomas; Chun, Jung-Ho; Dauparas, Justas; Bennett, Nathaniel; Wicky, Basile I. M.; Muenks, Andrew; DiMaio, Frank; Correia, Bruno; Ovchinnikov, Sergey; Baker, David

Scaffolding protein functional sites using deep learning Journal Article

In: Science, 2022.

Abstract | Links | BibTeX

2.

Lovelock, Sarah L.; Crawshaw, Rebecca; Basler, Sophie; Levy, Colin; Baker, David; Hilvert, Donald; Green, Anthony P.

The road to fully programmable protein catalysis Journal Article

In: Nature, 2022.

Abstract | Links | BibTeX

3.

Zhang, Jason Z.; Yeh, Hsien-Wei; Walls, Alexandra C.; Wicky, Basile I. M.; Sprouse, Kaitlin R.; VanBlargan, Laura A.; Treger, Rebecca; Quijano-Rubio, Alfredo; Pham, Minh N.; Kraft, John C.; Haydon, Ian C.; Yang, Wei; DeWitt, Michelle; Bowen, John E.; Chow, Cameron M.; Carter, Lauren; Ravichandran, Rashmi; Wener, Mark H.; Stewart, Lance; Veesler, David; Diamond, Michael S.; Greninger, Alexander L.; Koelle, David M.; Baker, David

Thermodynamically coupled biosensors for detecting neutralizing antibodies against SARS-CoV-2 variants Journal Article

In: Nature Biotechnology, 2022.

Abstract | Links | BibTeX

4.

Hunt, Andrew C.; Case, James Brett; Park, Young-Jun; Cao, Longxing; Wu, Kejia; Walls, Alexandra C.; Liu, Zhuoming; Bowen, John E.; Yeh, Hsien-Wei; Saini, Shally; Helms, Louisa; Zhao, Yan Ting; Hsiang, Tien-Ying; Starr, Tyler N.; Goreshnik, Inna; Kozodoy, Lisa; Carter, Lauren; Ravichandran, Rashmi; Green, Lydia B.; Matochko, Wadim L.; Thomson, Christy A.; Vögeli, Bastian; Krüger, Antje; VanBlargan, Laura A.; Chen, Rita E.; Ying, Baoling; Bailey, Adam L.; Kafai, Natasha M.; Boyken, Scott E.; Ljubetič, Ajasja; Edman, Natasha; Ueda, George; Chow, Cameron M.; Johnson, Max; Addetia, Amin; Navarro, Mary Jane; Panpradist, Nuttada; Gale, Michael; Freedman, Benjamin S.; Bloom, Jesse D.; Ruohola-Baker, Hannele; Whelan, Sean P. J.; Stewart, Lance; Diamond, Michael S.; Veesler, David; Jewett, Michael C.; Baker, David

Multivalent designed proteins neutralize SARS-CoV-2 variants of concern and confer protection against infection in mice Journal Article

In: Science Translational Medicine, 2022.

Abstract | Links | BibTeX

5.

Fujioka, Toshifumi; Numoto, Nobutaka; Akama, Hiroyuki; Shilpa, Kola; Oka, Michiko; Roy, Prodip K.; Krishna, Yarkali; Ito, Nobutoshi; Baker, David; Oda, Masayuki; Tanaka, Fujie

Varying the Directionality of Protein Catalysts for Aldol and Retro-Aldol Reactions Journal Article

In: ChemBioChem, vol. 23, no. 2, pp. e202100435, 2022.

Abstract | Links | BibTeX

6.

Crawshaw, Rebecca; Crossley, Amy E.; Johannissen, Linus; Burke, Ashleigh J.; Hay, Sam; Levy, Colin; Baker, David; Lovelock, Sarah L.; Green, Anthony P.

Engineering an efficient and enantioselective enzyme for the Morita-Baylis-Hillman reaction Journal Article

In: Nature Chemistry, 2021.

Abstract | Links | BibTeX

7.

Legler, Patricia M.; Little, Stephen F.; Senft, Jeffrey; Schokman, Rowena; Carra, John H.; Compton, Jaimee R.; Chabot, Donald; Tobery, Steven; Fetterer, David P.; Siegel, Justin B.; Baker, David; Friedlander, Arthur M.

Treatment of experimental anthrax with pegylated circularly permuted capsule depolymerase Journal Article

In: Science Translational Medicine, 2021.

Abstract | Links | BibTeX

8.

Hosseinzadeh, Parisa; Watson, Paris R.; Craven, Timothy W.; Li, Xinting; Rettie, Stephen; Pardo-Avila, Fátima; Bera, Asim K.; Mulligan, Vikram Khipple; Lu, Peilong; Ford, Alexander S.; Weitzner, Brian D.; Stewart, Lance J.; Moyer, Adam P.; Di Piazza, Maddalena; Whalen, Joshua G.; Greisen, Per Jr.; Christianson, David W.; Baker, David

Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites Journal Article

In: Nature Communications, 2021.

Abstract | Links | BibTeX

9.

Divine, Robby; Dang, Ha V.; Ueda, George; Fallas, Jorge A.; Vulovic, Ivan; Sheffler, William; Saini, Shally; Zhao, Yan Ting; Raj, Infencia Xavier; Morawski, Peter A.; Jennewein, Madeleine F.; Homad, Leah J.; Wan, Yu-Hsin; Tooley, Marti R.; Seeger, Franziska; Etemadi, Ali; Fahning, Mitchell L.; Lazarovits, James; Roederer, Alex; Walls, Alexandra C.; Stewart, Lance; Mazloomi, Mohammadali; King, Neil P.; Campbell, Daniel J.; McGuire, Andrew T.; Stamatatos, Leonidas; Ruohola-Baker, Hannele; Mathieu, Julie; Veesler, David; Baker, David

Designed proteins assemble antibodies into modular nanocages Journal Article

In: Science, vol. 372, no. 6537, 2021.

Abstract | Links | BibTeX

10.

Mulligan, Vikram Khipple; Workman, Sean; Sun, Tianjun; Rettie, Stephen; Li, Xinting; Worrall, Liam J.; Craven, Timothy W.; King, Dustin T.; Hosseinzadeh, Parisa; Watkins, Andrew M.; Renfrew, P. Douglas; Guffy, Sharon; Labonte, Jason W.; Moretti, Rocco; Bonneau, Richard; Strynadka, Natalie C. J.; Baker, David

Computationally designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1 Journal Article

In: Proceedings of the National Academy of Sciences, vol. 118, no. 12, 2021.

Abstract | Links | BibTeX

11.

Basanta, Benjamin; Bick, Matthew J.; Bera, Asim K.; Norn, Christoffer; Chow, Cameron M.; Carter, Lauren P.; Goreshnik, Inna; Dimaio, Frank; Baker, David

An enumerative algorithm for de novo design of proteins with diverse pocket structures Journal Article

In: Proceedings of the National Academy of Sciences, vol. 117, no. 36, pp. 22135–22145, 2020, ISBN: 0027-8424.

Abstract | Links | BibTeX

12.

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

13.

Yakov Kipnis Brian D. Weitzner, A. Gerard Daniel

A computational method for design of connected catalytic networks in proteins Journal Article

In: Protein Science, 2019.

Abstract | Links | BibTeX

14.

Romero Romero, Maria Luisa; Yang, Fan; Lin, Yu-Ru; Toth-Petroczy, Agnes; Berezovsky, Igor N.; Goncearenco, Alexander; Yang, Wen; Wellner, Alon; Kumar-Deshmukh, Fanindra; Sharon, Michal; Baker, David; Varani, Gabriele; Tawfik, Dan S.

Simple yet functional phosphate-loop proteins Journal Article

In: PNAS, vol. 115, no. 51, pp. E11943–E11950, 2018, ISSN: 0027-8424.

Abstract | Links | BibTeX

15.

Yue-Ting K. Lau,; Vladimir Baytshtok,; Tessa A. Howard,; Brooke M. Fiala,; JayLee M. Johnson,; Lauren P. Carter,; David Baker,; Christopher D. Lima,; Bahl, Christopher D.

Discovery and engineering of enhanced SUMO protease enzymes Journal Article

In: The Journal of Biological Chemistry, vol. 293, pp. 13224-13233, 2018.

Abstract | Links | BibTeX

16.

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

17.

Marcos, Enrique*; Basanta, Benjamin*; Chidyausiku, Tamuka M.; Tang, Yuefeng; Oberdorfer, Gustav; Liu, Gaohua; Swapna, G. V. T.; Guan, Rongjin; Silva, Daniel-Adriano; Dou, Jiayi; Pereira, Jose Henrique; Xiao, Rong; Sankaran, Banumathi; Zwart, Peter H.; Montelione, Gaetano T.; Baker, David

Principles for designing proteins with cavities formed by curved β sheets Journal Article

In: Science, vol. 355, no. 6321, pp. 201–206, 2017, ISSN: 0036-8075.

Abstract | Links | BibTeX

18.

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

19.

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

20.

Goldsmith, M; Eckstein, S; Ashani, Y; Greisen, P Jr; Leader, H; Sussman, JL; Aggarwal, N; Ovchinnikov, S; Tawfik, DS; Baker, D; Thiermann, H; Worek, F

Catalytic efficiencies of directly evolved phosphotriesterase variants with structurally different organophosphorus compounds in vitro Journal Article

In: Archives of Toxicology, 2015.

Abstract | Links | BibTeX

77 entries « 1 of 4 »

 

2022

FROM THE LAB

Show all

Jue Wang, Sidney Lisanza, David Juergens, Doug Tischer, Joseph L. Watson, Karla M. Castro, Robert Ragotte, Amijai Saragovi, Lukas F. Milles, Minkyung Baek, Ivan Anishchenko, Wei Yang, Derrick R. Hicks, Marc Expòsit, Thomas Schlichthaerle, Jung-Ho Chun, Justas Dauparas, Nathaniel Bennett, Basile I. M. Wicky, Andrew Muenks, Frank DiMaio, Bruno Correia, Sergey Ovchinnikov, David Baker

Scaffolding protein functional sites using deep learning Journal Article

In: Science, 2022.

Abstract | Links

Zhang, Jason Z. and Yeh, Hsien-Wei and Walls, Alexandra C. and Wicky, Basile I. M. and Sprouse, Kaitlin R. and VanBlargan, Laura A. and Treger, Rebecca and Quijano-Rubio, Alfredo and Pham, Minh N. and Kraft, John C. and Haydon, Ian C. and Yang, Wei and DeWitt, Michelle and Bowen, John E. and Chow, Cameron M. and Carter, Lauren and Ravichandran, Rashmi and Wener, Mark H. and Stewart, Lance and Veesler, David and Diamond, Michael S. and Greninger, Alexander L. and Koelle, David M. and Baker, David

Thermodynamically coupled biosensors for detecting neutralizing antibodies against SARS-CoV-2 variants Journal Article

In: Nature Biotechnology, 2022.

Abstract | Links

Andrew C. Hunt, James Brett Case, Young-Jun Park, Longxing Cao, Kejia Wu, Alexandra C. Walls, Zhuoming Liu, John E. Bowen, Hsien-Wei Yeh, Shally Saini, Louisa Helms, Yan Ting Zhao, Tien-Ying Hsiang, Tyler N. Starr, Inna Goreshnik, Lisa Kozodoy, Lauren Carter, Rashmi Ravichandran, Lydia B. Green, Wadim L. Matochko, Christy A. Thomson, Bastian Vögeli, Antje Krüger, Laura A. VanBlargan, Rita E. Chen, Baoling Ying, Adam L. Bailey, Natasha M. Kafai, Scott E. Boyken, Ajasja Ljubetič, Natasha Edman, George Ueda, Cameron M. Chow, Max Johnson, Amin Addetia, Mary Jane Navarro, Nuttada Panpradist, Michael Gale, Benjamin S. Freedman, Jesse D. Bloom, Hannele Ruohola-Baker, Sean P. J. Whelan, Lance Stewart, Michael S. Diamond, David Veesler, Michael C. Jewett, David Baker

Multivalent designed proteins neutralize SARS-CoV-2 variants of concern and confer protection against infection in mice Journal Article

In: Science Translational Medicine, 2022.

Abstract | Links

COLLABORATOR LED

Show all

Sarah L. Lovelock, Rebecca Crawshaw, Sophie Basler, Colin Levy, David Baker, Donald Hilvert, Anthony P. Green

The road to fully programmable protein catalysis Journal Article

In: Nature, 2022.

Abstract | Links

Toshifumi Fujioka, Nobutaka Numoto, Hiroyuki Akama, Kola Shilpa, Michiko Oka, Prodip K. Roy, Yarkali Krishna, Nobutoshi Ito, David Baker, Masayuki Oda, Fujie Tanaka

Varying the Directionality of Protein Catalysts for Aldol and Retro-Aldol Reactions Journal Article

In: ChemBioChem, vol. 23, no. 2, pp. e202100435, 2022.

Abstract | Links

2021

FROM THE LAB

Show all

Hosseinzadeh, Parisa and Watson, Paris R. and Craven, Timothy W. and Li, Xinting and Rettie, Stephen and Pardo-Avila, Fátima and Bera, Asim K. and Mulligan, Vikram Khipple and Lu, Peilong and Ford, Alexander S. and Weitzner, Brian D. and Stewart, Lance J. and Moyer, Adam P. and Di Piazza, Maddalena and Whalen, Joshua G. and Greisen, Per Jr. and Christianson, David W. and Baker, David

Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites Journal Article

In: Nature Communications, 2021.

Abstract | Links

Divine, Robby, Dang, Ha V., Ueda, George, Fallas, Jorge A., Vulovic, Ivan, Sheffler, William, Saini, Shally, Zhao, Yan Ting, Raj, Infencia Xavier, Morawski, Peter A., Jennewein, Madeleine F., Homad, Leah J., Wan, Yu-Hsin, Tooley, Marti R., Seeger, Franziska, Etemadi, Ali, Fahning, Mitchell L., Lazarovits, James, Roederer, Alex, Walls, Alexandra C., Stewart, Lance, Mazloomi, Mohammadali, King, Neil P., Campbell, Daniel J., McGuire, Andrew T., Stamatatos, Leonidas, Ruohola-Baker, Hannele, Mathieu, Julie, Veesler, David, Baker, David

Designed proteins assemble antibodies into modular nanocages Journal Article

In: Science, vol. 372, no. 6537, 2021.

Abstract | Links

Mulligan, Vikram Khipple, Workman, Sean, Sun, Tianjun, Rettie, Stephen, Li, Xinting, Worrall, Liam J., Craven, Timothy W., King, Dustin T., Hosseinzadeh, Parisa, Watkins, Andrew M., Renfrew, P. Douglas, Guffy, Sharon, Labonte, Jason W., Moretti, Rocco, Bonneau, Richard, Strynadka, Natalie C. J., Baker, David

Computationally designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1 Journal Article

In: Proceedings of the National Academy of Sciences, vol. 118, no. 12, 2021.

Abstract | Links

COLLABORATOR LED

Show all

Crawshaw, Rebecca and Crossley, Amy E. and Johannissen, Linus and Burke, Ashleigh J. and Hay, Sam and Levy, Colin and Baker, David and Lovelock, Sarah L. and Green, Anthony P.

Engineering an efficient and enantioselective enzyme for the Morita-Baylis-Hillman reaction Journal Article

In: Nature Chemistry, 2021.

Abstract | Links

Patricia M. Legler and Stephen F. Little and Jeffrey Senft and Rowena Schokman and John H. Carra and Jaimee R. Compton and Donald Chabot and Steven Tobery and David P. Fetterer and Justin B. Siegel and David Baker and Arthur M. Friedlander

Treatment of experimental anthrax with pegylated circularly permuted capsule depolymerase Journal Article

In: Science Translational Medicine, 2021.

Abstract | Links

2020

FROM THE LAB

Show all

Basanta, Benjamin, Bick, Matthew J., Bera, Asim K., Norn, Christoffer, Chow, Cameron M., Carter, Lauren P., Goreshnik, Inna, Dimaio, Frank, Baker, David

An enumerative algorithm for de novo design of proteins with diverse pocket structures Journal Article

In: Proceedings of the National Academy of Sciences, vol. 117, no. 36, pp. 22135–22145, 2020, ISBN: 0027-8424.

Abstract | Links

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

Show all

Sorry, no publications matched your criteria.

2019

FROM THE LAB

Show all

Brian D. Weitzner, Yakov Kipnis, A. Gerard Daniel, Donald Hilvert, David Baker

A computational method for design of connected catalytic networks in proteins Journal Article

In: Protein Science, 2019.

Abstract | Links

COLLABORATOR LED

Show all

Sorry, no publications matched your criteria.

2018

FROM THE LAB

Show all

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

Romero Romero, Maria Luisa, Yang, Fan, Lin, Yu-Ru, Toth-Petroczy, Agnes, Berezovsky, Igor N., Goncearenco, Alexander, Yang, Wen, Wellner, Alon, Kumar-Deshmukh, Fanindra, Sharon, Michal, Baker, David, Varani, Gabriele, Tawfik, Dan S.

Simple yet functional phosphate-loop proteins Journal Article

In: PNAS, vol. 115, no. 51, pp. E11943–E11950, 2018, ISSN: 0027-8424.

Abstract | Links

Yue-Ting K. Lau,, Vladimir Baytshtok,, Tessa A. Howard,, Brooke M. Fiala,, JayLee M. Johnson,, Lauren P. Carter,, David Baker,, Christopher D. Lima,, Christopher D. Bahl

Discovery and engineering of enhanced SUMO protease enzymes Journal Article

In: The Journal of Biological Chemistry, vol. 293, pp. 13224-13233, 2018.

Abstract | Links

2017–1998

ALL PAPERS

Show all

61 entries « 1 of 3 »

2017

Marcos, Enrique*, Basanta, Benjamin*, Chidyausiku, Tamuka M., Tang, Yuefeng, Oberdorfer, Gustav, Liu, Gaohua, Swapna, G. V. T., Guan, Rongjin, Silva, Daniel-Adriano, Dou, Jiayi, Pereira, Jose Henrique, Xiao, Rong, Sankaran, Banumathi, Zwart, Peter H., Montelione, Gaetano T., Baker, David

Principles for designing proteins with cavities formed by curved β sheets Journal Article

In: Science, vol. 355, no. 6321, pp. 201–206, 2017, ISSN: 0036-8075.

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

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

M Goldsmith, S Eckstein, Y Ashani, P Jr Greisen, H Leader, JL Sussman, N Aggarwal, S Ovchinnikov, DS Tawfik, D Baker, H Thiermann, F Worek

Catalytic efficiencies of directly evolved phosphotriesterase variants with structurally different organophosphorus compounds in vitro Journal Article

In: Archives of Toxicology, 2015.

Abstract | Links

PS Huang, K Feldmeier, F Parmeggiani, DA Fernandez Velasco, B Höcker, D Baker

De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy Journal Article

In: Nature Chemical Biology, vol. 12(1), pp. 29-34, 2015.

Abstract | Links

Clancey Wolf, Justin B Siegel, Christine Tinberg, Alessandra Camarca, Carmen Gianfrani, Shirley Paski, Rongjin Guan, Gaetano T Montelione, David Baker, Ingrid S Pultz

Engineering of Kuma030: a gliadin peptidase that rapidly degrades immunogenic gliadin peptides in gastric conditions. Journal Article

In: Journal of the American Chemical Society, 2015, ISSN: 1520-5126.

Abstract | Links

Justin B Siegel, Amanda Lee Smith, Sean Poust, Adam J Wargacki, Arren Bar-Even, Catherine Louw, Betty W Shen, Christopher B Eiben, Huu M Tran, Elad Noor, Jasmine L Gallaher, Jacob Bale, Yasuo Yoshikuni, Michael H Gelb, Jay D Keasling, Barry L Stoddard, Mary E Lidstrom, David Baker

Computational protein design enables a novel one-carbon assimilation pathway Journal Article

In: Proceedings of the National Academy of Sciences of the United States of America, 2015, ISSN: 1091-6490.

Abstract | Links

Vinayak Vittal, Lei Shi, Dawn M Wenzel, K Matthew Scaglione, Emily D Duncan, Venkatesha Basrur, Kojo S J Elenitoba-Johnson, David Baker, Henry L Paulson, Peter S Brzovic, Rachel E Klevit

Intrinsic disorder drives N-terminal ubiquitination by Ube2w Journal Article

In: Nature Chemical Biology, vol. 11, pp. 83-9, 2015, ISSN: 1552-4469.

Abstract | Links

2014

Daniel S Liu, Lucas G Niv'on, Florian Richter, Peter J Goldman, Thomas J Deerinck, Jennifer Z Yao, Douglas Richardson, William S Phipps, Anne Z Ye, Mark H Ellisman, Catherine L Drennan, David Baker, Alice Y Ting

Computational design of a red fluorophore ligase for site-specific protein labeling in living cells. Journal Article

In: Proceedings of the National Academy of Sciences of the United States of America, vol. 111, pp. E4551-9, 2014, ISSN: 1091-6490.

Abstract | Links

Yu Liu, Xin Zhang, Yun Lei Tan, Gira Bhabha, Damian C Ekiert, Yakov Kipnis, Sinisa Bjelic, David Baker, Jeffery W Kelly

De novo-designed enzymes as small-molecule-regulated fluorescence imaging tags and fluorescent reporters. Journal Article

In: Journal of the American Chemical Society, vol. 136, pp. 13102-5, 2014, ISSN: 1520-5126.

Abstract | Links

Nathalie Preiswerk, Tobias Beck, Jessica D Schulz, Peter Milovn'ik, Clemens Mayer, Justin B Siegel, David Baker, Donald Hilvert

Impact of scaffold rigidity on the design and evolution of an artificial Diels-Alderase. Journal Article

In: Proceedings of the National Academy of Sciences of the United States of America, vol. 111, pp. 8013-8, 2014, ISSN: 1091-6490.

Abstract | Links

Sergey Ovchinnikov, Hetunandan Kamisetty, David Baker

Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information. Journal Article

In: eLife, vol. 3, pp. e02030, 2014, ISSN: 2050-084X.

Abstract | Links

Sridharan Rajagopalan, Chu Wang, Kai Yu, Alexandre P Kuzin, Florian Richter, Scott Lew, Aleksandr E Miklos, Megan L Matthews, Jayaraman Seetharaman, Min Su, John F Hunt, Benjamin F Cravatt, David Baker

Design of activated serine-containing catalytic triads with atomic-level accuracy Journal Article

In: Nature chemical biology, vol. 10, pp. 386-391, 2014, ISSN: 1552-4469.

Abstract | Links

Yupeng Wang, Iram F Khan, Sandrine Boissel, Jordan Jarjour, Joseph Pangallo, Summer Thyme, David Baker, Andrew M Scharenberg, David J Rawlings

Progressive engineering of a homing endonuclease genome editing reagent for the murine X-linked immunodeficiency locus. Journal Article

In: Nucleic acids research, 2014, ISSN: 1362-4962.

Abstract | Links

Yu Liu, Yun Lei Tan, Xin Zhang, Gira Bhabha, Damian C Ekiert, Joseph C Genereux, Younhee Cho, Yakov Kipnis, Sinisa Bjelic, David Baker, Jeffery W Kelly

Small molecule probes to quantify the functional fraction of a specific protein in a cell with minimal folding equilibrium shifts. Journal Article

In: Proceedings of the National Academy of Sciences of the United States of America, 2014, ISSN: 1091-6490.

Abstract | Links

Hein J Wijma, Robert J Floor, Peter A Jekel, David Baker, Siewert J Marrink, Dick B Janssen

Computationally designed libraries for rapid enzyme stabilization. Journal Article

In: Protein engineering, design & selection : PEDS, vol. 27, pp. 49-58, 2014, ISSN: 1741-0134.

Abstract | Links

Tyler D Shropshire, Jack Reifert, Sridharan Rajagopalan, David Baker, Stuart C Feinstein, Patrick S Daugherty

Amyloid β peptide cleavage by kallikrein 7 attenuates fibril growth and rescues neurons from Aβ-mediated toxicity in vitro. Journal Article

In: Biological chemistry, vol. 395, pp. 109-18, 2014, ISSN: 1437-4315.

Abstract | Links

Summer Thyme, David Baker

Redesigning the Specificity of Protein-DNA Interactions with Rosetta. Journal Article

In: Methods in molecular biology (Clifton, N.J.), vol. 1123, pp. 265-82, 2014, ISSN: 1940-6029.

Abstract | Links

2013

Izhack Cherny, Per Greisen, Yacov Ashani, Sagar D Khare, Gustav Oberdorfer, Haim Leader, David Baker, Dan S Tawfik

Engineering V-type nerve agents detoxifying enzymes using computationally focused libraries Journal Article

In: ACS chemical biology, vol. 8, pp. 2394-403, 2013, ISSN: 1554-8937.

Abstract | Links

Lucas G Niv'on, Sinisa Bjelic, Chris King, David Baker

Automating human intuition for protein design Journal Article

In: Proteins, 2013, ISSN: 1097-0134.

Abstract | Links

Erik Procko, Rickard Hedman, Keith Hamilton, Jayaraman Seetharaman, Sarel J Fleishman, Min Su, James Aramini, Gregory Kornhaber, John F Hunt, Liang Tong, Gaetano T Montelione, David Baker

Computational design of a protein-based enzyme inhibitor. Journal Article

In: Journal of molecular biology, vol. 425, pp. 3563-75, 2013, ISSN: 1089-8638.

Abstract | Links

Jeremy H Mills, Sagar D Khare, Jill M Bolduc, Farhad Forouhar, Vikram Khipple Mulligan, Scott Lew, Jayaraman Seetharaman, Liang Tong, Barry L Stoddard, David Baker

Computational design of an unnatural amino acid dependent metalloprotein with atomic level accuracy. Journal Article

In: Journal of the American Chemical Society, vol. 135, pp. 13393-9, 2013, ISSN: 1520-5126.

Abstract | Links

Lars Giger, Sami Caner, Richard Obexer, Peter Kast, David Baker, Nenad Ban, Donald Hilvert

Evolution of a designed retro-aldolase leads to complete active site remodeling. Journal Article

In: Nature chemical biology, vol. 9, pp. 494-8, 2013, ISSN: 1552-4469.

Abstract | Links

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

Computational enzyme design Journal Article

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

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

Lucas Gregorio Niv'on, Rocco Moretti, David Baker

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

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

Abstract | Links

2012

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

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

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

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

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

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

Yakov Kipnis, David Baker

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

61 entries « 1 of 3 »