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84 entries « 1 of 5 »
1.

Craven, Timothy W.; Nolan, Mark D.; Bailey, Jonathan; Olatunji, Samir; Bann, Samantha J.; Bowen, Katherine; Ostrovitsa, Nikita; Costa, Thaina M. Da; Ballantine, Ross D.; Weichert, Dietmar; Levine, Paul M.; Stewart, Lance J.; Bhardwaj, Gaurav; Geoghegan, Joan A.; Cochrane, Stephen A.; Scanlan, Eoin M.; Caffrey, Martin; Baker, David

Computational Design of Cyclic Peptide Inhibitors of a Bacterial Membrane Lipoprotein Peptidase Journal Article

In: ACS Chemical Biology, 2024.

Abstract | Links | BibTeX

2.

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

3.

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

4.

Kalvet, Indrek; Ortmayer, Mary; Zhao, Jingming; Crawshaw, Rebecca; Ennist, Nathan M.; Levy, Colin; Roy, Anindya; Green, Anthony P.; Baker, David

Design of Heme Enzymes with a Tunable Substrate Binding Pocket Adjacent to an Open Metal Coordination Site Journal Article

In: J. Am. Chem. Soc., 2023.

Abstract | Links | BibTeX

5.

Watson, Paris R.; Gupta, Suchetana; Hosseinzadeh, Parisa; Brown, Benjamin P.; Baker, David; Christianson, David W.

Macrocyclic Octapeptide Binding and Inferences on Protein Substrate Binding to Histone Deacetylase 6 Journal Article

In: ACS Chemical Biology, 2023.

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6.

Andy Hsien-Wei Norn Yeh, Christoffer Kipnis

De novo design of luciferases using deep learning Journal Article

In: Nature, 2023.

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7.

Kipnis, Yakov; Chaib, Anissa Ouald; Vorobieva, Anastassia A.; Cai, Guangyang; Reggiano, Gabriella; Basanta, Benjamin; Kumar, Eshan; Mittl, Peer R. E.; Hilvert, Donald; Baker, David

Design and optimization of enzymatic activity in a de novo β-barrel scaffold Journal Article

In: Protein Science, 2022.

Abstract | Links | BibTeX

8.

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.

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9.

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.

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10.

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

11.

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

12.

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

13.

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

14.

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

15.

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

16.

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

17.

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

18.

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

19.

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

20.

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

84 entries « 1 of 5 »