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21 entries « 1 of 2 »
1.

Jiang, Hanlun; Jude, Kevin M.; Wu, Kejia; Fallas, Jorge; Ueda, George; Brunette, T. J.; Hicks, Derrick R.; Pyles, Harley; Yang, Aerin; Carter, Lauren; Lamb, Mila; Li, Xinting; Levine, Paul M.; Stewart, Lance; Garcia, K. Christopher; Baker, David

De novo design of buttressed loops for sculpting protein functions Journal Article

In: Nature Chemical Biology, 2024.

Abstract | Links | BibTeX

2.

Sahtoe, Danny D.; Andrzejewska, Ewa A.; Han, Hannah L.; Rennella, Enrico; Schneider, Matthias M.; Meisl, Georg; Ahlrichs, Maggie; Decarreau, Justin; Nguyen, Hannah; Kang, Alex; Levine, Paul; Lamb, Mila; Li, Xinting; Bera, Asim K.; Kay, Lewis E.; Knowles, Tuomas P. J.; Baker, David

Design of amyloidogenic peptide traps Journal Article

In: Nature Chemical Biology, 2024.

Abstract | Links | BibTeX

3.

Mateos, Diego Lopez; Murray, Adam M.; Nguyen, Hai M.; Venkatesh, Preetham; Koepnick, Brian; Baker, David; Wulff, Heike; Yarov-Yarovoy, Vladimir

Computational design of binders targeting the VSDIV from NaV1.7 sodium channel Journal Article

In: Biophysical Journal, 2024.

Abstract | Links | BibTeX

4.

Torres, Susana Vázquez; Leung, Philip J Y; Venkatesh, Preetham; Lutz, Isaac D; Hink, Fabian; Huynh, Huu-Hien; Becker, Jessica; Yeh, Andy Hsien-Wei; Juergens, David; Bennett, Nathaniel R; Hoofnagle, Andrew N; Huang, Eric; MacCoss, Michael J; Expòsit, Marc; Lee, Gyu Rie; Bera, Asim K; Kang, Alex; Cruz, Joshmyn De La; Levine, Paul M; Li, Xinting; Lamb, Mila; Gerben, Stacey R; Murray, Analisa; Heine, Piper; Korkmaz, Elif Nihal; Nivala, Jeff; Stewart, Lance; Watson, Joseph L; Rogers, Joseph M; Baker, David

De novo design of high-affinity binders of bioactive helical peptides Journal Article

In: Nature, 2023, ISSN: 1476-4687.

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5.

Hicks DR An L, Zorine D

Hallucination of closed repeat proteins containing central pockets Journal Article

In: Nature Structural & Molecular Biology, 2023.

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6.

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

7.

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.

Abstract | Links | BibTeX

8.

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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9.

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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10.

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.

Abstract | Links | BibTeX

11.

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.

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12.

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

13.

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

14.

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

15.

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

16.

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

17.

Holstein, Carly A; Chevalier, Aaron; Bennett, Steven; Anderson, Caitlin E; Keniston, Karen; Olsen, Cathryn; Li, Bing; Bales, Brian; Moore, David R; Fu, Elain; Baker, David; Yager, Paul

Immobilizing affinity proteins to nitrocellulose: a toolbox for paper-based assay developers. Journal Article

In: Analytical and bioanalytical chemistry, 2015, ISSN: 1618-2650.

Abstract | Links | BibTeX

18.

Moretti, Rocco; Fleishman, Sarel J; Agius, Rudi; Torchala, Mieczyslaw; Bates, Paul A; Kastritis, Panagiotis L; ao P G L M Rodrigues, Jo; Trellet, Mika"el; Bonvin, Alexandre M J J; Cui, Meng; Rooman, Marianne; Gillis, Dimitri; Dehouck, Yves; Moal, Iain; Romero-Durana, Miguel; Perez-Cano, Laura; Pallara, Chiara; Jimenez, Brian; Fernandez-Recio, Juan; Flores, Samuel; Pacella, Michael; Kilambi, Krishna Praneeth; Gray, Jeffrey J; Popov, Petr; Grudinin, Sergei; Esquivel-Rodr’iguez, Juan; Kihara, Daisuke; Zhao, Nan; Korkin, Dmitry; Zhu, Xiaolei; Demerdash, Omar N A; Mitchell, Julie C; Kanamori, Eiji; Tsuchiya, Yuko; Nakamura, Haruki; Lee, Hasup; Park, Hahnbeom; Seok, Chaok; Sarmiento, Jamica; Liang, Shide; Teraguchi, Shusuke; Standley, Daron M; Shimoyama, Hiromitsu; Terashi, Genki; Takeda-Shitaka, Mayuko; Iwadate, Mitsuo; Umeyama, Hideaki; Beglov, Dmitri; Hall, David R; Kozakov, Dima; Vajda, Sandor; Pierce, Brian G; Hwang, Howook; Vreven, Thom; Weng, Zhiping; Huang, Yangyu; Li, Haotian; Yang, Xiufeng; Ji, Xiaofeng; Liu, Shiyong; Xiao, Yi; Zacharias, Martin; Qin, Sanbo; Zhou, Huan-Xiang; Huang, Sheng-You; Zou, Xiaoqin; Velankar, Sameer; Janin, Jo"el; Wodak, Shoshana J; Baker, David

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Journal Article

In: Proteins, vol. 81, pp. 1980-7, 2013, ISSN: 1097-0134.

Abstract | Links | BibTeX

19.

Tinberg, Christine E; Khare, Sagar D; Dou, Jiayi; Doyle, Lindsey; Nelson, Jorgen W; Schena, Alberto; Jankowski, Wojciech; Kalodimos, Charalampos G; Johnsson, Kai; Stoddard, Barry L; Baker, David

Computational design of ligand-binding proteins with high affinity and selectivity Journal Article

In: Nature, vol. 501, pp. 212-6, 2013, ISSN: 1476-4687.

Abstract | Links | BibTeX

20.

Whitehead, Timothy A; Baker, David; Fleishman, Sarel J

Computational design of novel protein binders and experimental affinity maturation Journal Article

In: Methods in enzymology, vol. 523, pp. 1-19, 2013, ISSN: 1557-7988.

Abstract | Links | BibTeX

21 entries « 1 of 2 »