Publications

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27 entries « 1 of 2 »
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.

Watson, Joseph L.; Juergens, David; Bennett, Nathaniel R.; Trippe, Brian L.; Yim, Jason; Eisenach, Helen E.; Ahern, Woody; Borst, Andrew J.; Ragotte, Robert J.; Milles, Lukas F.; Wicky, Basile I. M.; Hanikel, Nikita; Pellock, Samuel J.; Courbet, Alexis; Sheffler, William; Wang, Jue; Venkatesh, Preetham; Sappington, Isaac; Torres, Susana Vázquez; Lauko, Anna; De Bortoli, Valentin; Mathieu, Emile; Ovchinnikov, Sergey; Barzilay, Regina; Jaakkola, Tommi S.; DiMaio, Frank; Baek, Minkyung; Baker, David

De novo design of protein structure and function with RFdiffusion Journal Article

In: Nature, 2023.

Abstract | Links | BibTeX

3.

Bennett, Nathaniel R.; Coventry, Brian; Goreshnik, Inna; Huang, Buwei; Allen, Aza; Vafeados, Dionne; Peng, Ying Po; Dauparas, Justas; Baek, Minkyung; Stewart, Lance; DiMaio, Frank; De Munck, Steven; Savvides, Savvas N.; Baker, David

Improving de novo protein binder design with deep learning Journal Article

In: Nature Communications, 2023.

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4.

Danny D. Sahtoe Enrico Rennella, David Baker; Kay, Lewis E.

Exploiting conformational dynamics to modulate the function of designed proteins Journal Article

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

Abstract | Links | BibTeX

5.

Kim, David E.; Jensen, Davin R.; Feldman, David; Tischer, Doug; Saleem, Ayesha; Chow, Cameron M.; Li, Xinting; Carter, Lauren; Milles, Lukas; Nguyen, Hannah; Kang, Alex; Bera, Asim K.; Peterson, Francis C.; Volkman, Brian F.; Ovchinnikov, Sergey; Baker, David

De novo design of small beta barrel proteins Journal Article

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

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6.

Gerben, Stacey R; Borst, Andrew J; Hicks, Derrick R; Moczygemba, Isabelle; Feldman, David; Coventry, Brian; Yang, Wei; Bera, Asim K.; Miranda, Marcos; Kang, Alex; Nguyen, Hannah; Baker, David

Design of Diverse Asymmetric Pockets in De Novo Homo-oligomeric Proteins Journal Article

In: Biochemistry, 2023.

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7.

Agarwal, Dilip Kumar; Hunt, Andrew C.; Shekhawat, Gajendra S.; Carter, Lauren; Chan, Sidney; Wu, Kejia; Cao, Longxing; Baker, David; Lorenzo-Redondo, Ramon; Ozer, Egon A.; Simons, Lacy M.; Hultquist, Judd F.; Jewett, Michael C.; Dravid, Vinayak P.

Rapid and Sensitive Detection of Antigen from SARS-CoV-2 Variants of Concern by a Multivalent Minibinder-Functionalized Nanomechanical Sensor Journal Article

In: Analytical Chemistry, 2022.

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8.

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.

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9.

Cao, Longxing; Coventry, Brian; Goreshnik, Inna; Huang, Buwei; Park, Joon Sung; Jude, Kevin M.; Marković, Iva; Kadam, Rameshwar U.; Verschueren, Koen H. G.; Verstraete, Kenneth; Walsh, Scott Thomas Russell; Bennett, Nathaniel; Phal, Ashish; Yang, Aerin; Kozodoy, Lisa; DeWitt, Michelle; Picton, Lora; Miller, Lauren; Strauch, Eva-Maria; DeBouver, Nicholas D.; Pires, Allison; Bera, Asim K.; Halabiya, Samer; Hammerson, Bradley; Yang, Wei; Bernard, Steffen; Stewart, Lance; Wilson, Ian A.; Ruohola-Baker, Hannele; Schlessinger, Joseph; Lee, Sangwon; Savvides, Savvas N.; Garcia, K. Christopher; Baker, David

Design of protein binding proteins from target structure alone Journal Article

In: Nature, 2022.

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10.

Levy, Shiri; Somasundaram, Logeshwaran; Raj, Infencia Xavier; Ic-Mex, Diego; Phal, Ashish; Schmidt, Sven; Ng, Weng I.; Mar, Daniel; Decarreau, Justin; Moss, Nicholas; Alghadeer, Ammar; Honkanen, Henrik; Sarthy, Jay; Vitanza, Nicholas; Hawkins, R. David; Mathieu, Julie; Wang, Yuliang; Baker, David; Bomsztyk, Karol; Ruohola-Baker, Hannele

dCas9 fusion to computer-designed PRC2 inhibitor reveals functional TATA box in distal promoter region Journal Article

In: Cell Reports, 2022.

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11.

Bryan, Cassie M.; Rocklin, Gabriel J.; Bick, Matthew J.; Ford, Alex; Majri-Morrison, Sonia; Kroll, Ashley V.; Miller, Chad J.; Carter, Lauren; Goreshnik, Inna; Kang, Alex; DiMaio, Frank; Tarbell, Kristin V.; Baker, David

Computational design of a synthetic PD-1 agonist Journal Article

In: Proceedings of the National Academy of Sciences, vol. 118, no. 29, 2021.

Abstract | Links | BibTeX

12.

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

13.

Sahtoe, Danny D.; Coscia, Adrian; Mustafaoglu, Nur; Miller, Lauren M.; Olal, Daniel; Vulovic, Ivan; Yu, Ta-Yi; Goreshnik, Inna; Lin, Yu-Ru; Clark, Lars; Busch, Florian; Stewart, Lance; Wysocki, Vicki H.; Ingber, Donald E.; Abraham, Jonathan; Baker, David

Transferrin receptor targeting by de novo sheet extension Journal Article

In: Proceedings of the National Academy of Sciences, 2021.

Abstract | Links | BibTeX

14.

Quijano-Rubio, Alfredo; Yeh, Hsien-Wei; Park, Jooyoung; Lee, Hansol; Langan, Robert A.; Boyken, Scott E.; Lajoie, Marc J.; Cao, Longxing; Chow, Cameron M.; Miranda, Marcos C.; Wi, Jimin; Hong, Hyo Jeong; Stewart, Lance; Oh, Byung-Ha; Baker, David

De novo design of modular and tunable protein biosensors Journal Article

In: Nature, 2021.

Abstract | Links | BibTeX

15.

Cao, Longxing; Goreshnik, Inna; Coventry, Brian; Case, James Brett; Miller, Lauren; Kozodoy, Lisa; Chen, Rita E.; Carter, Lauren; Walls, Alexandra C.; Park, Young-Jun; Strauch, Eva-Maria; Stewart, Lance; Diamond, Michael S.; Veesler, David; Baker, David

De novo design of picomolar SARS-CoV-2 miniprotein inhibitors Journal Article

In: Science, 2020.

Abstract | Links | BibTeX

16.

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

17.

Brunette, TJ; Bick, Matthew J.; Hansen, Jesse M.; Chow, Cameron M.; Kollman, Justin M.; Baker, David

Modular repeat protein sculpting using rigid helical junctions Journal Article

In: Proceedings of the National Academy of Sciences, 2020.

Abstract | Links | BibTeX

18.

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

19.

Silva, Daniel-Adriano; Stewart, Lance; Lam, Kwok-Ho; Jin, Rongsheng; Baker, David

Structures and disulfide cross‐linking of de novo designed therapeutic mini‐proteins Journal Article

In: FEBS Journal, vol. 285, no. 10, pp. 1783-1785, 2018.

Abstract | Links | BibTeX

20.

Chevalier*, Aaron; Silva*, Daniel-Adriano; Rocklin*, Gabriel J.; Hicks, Derrick R.; Vergara, Renan; Murapa, Patience; Bernard, Steffen M.; Zhang, Lu; Lam, Kwok-Ho; Yao, Guorui; Bahl, Christopher D.; Miyashita, Shin-Ichiro; Goreshnik, Inna; Fuller, James T.; Koday, Merika T.; Jenkins, Cody M.; Colvin, Tom; Carter, Lauren; Bohn, Alan; Bryan, Cassie M.; Fernández-Velasco, D. Alejandro; Stewart, Lance; Dong, Min; Huang, Xuhui; Jin, Rongsheng; Wilson, Ian A.; Fuller, Deborah H.; Baker, David

Massively parallel de novo protein design for targeted therapeutics Journal Article

In: Nature, vol. 550, no. 7674, pp. 74-79, 2017, ISSN: 0028-0836.

Abstract | Links | BibTeX

27 entries « 1 of 2 »