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500 entries « 1 of 10 »

2021

Woodall, Nicholas B; Weinberg, Zara ; Park, Jesslyn ; Busch, Florian ; Johnson, Richard S; Feldbauer, Mikayla J; Murphy, Michael ; Ahlrichs, Maggie ; Yousif, Issa ; MacCoss, Michael J; Wysocki, Vicki H; El-Samad, Hana ; Baker, David

De novo design of tyrosine and serine kinase-driven protein switches Journal Article

Nature Structural & Molecular Biology, 28 , pp. 762-770, 2021.

Abstract | Links | BibTeX

Baek, Minkyung; Anishchenko, Ivan; Park, Hahnbeom; Humphreys, Ian R; Baker, David

Protein oligomer modeling guided by predicted inter-chain contacts in CASP14 Journal Article

Proteins, 2021.

Abstract | Links | BibTeX

Baek, Minkyung ; DiMaio, Frank ; Anishchenko, Ivan ; Dauparas, Justas ; Ovchinnikov, Sergey ; Lee, Gyu Rie ; Wang, Jue ; Cong, Qian ; Kinch, Lisa N; Schaeffer, Dustin R; Millán, Claudia ; Park, Hahnbeom ; Adams, Carson ; Glassman, Caleb R; DeGiovanni, Andy ; Pereira, Jose H; Rodrigues, Andria V; van Dijk, Alberdina A; Ebrecht, Ana C; Opperman, Diederik J; Sagmeister, Theo ; Buhlheller, Christoph ; Pavkov-Keller, Tea ; Rathinaswamy, Manoj K; Dalwadi, Udit ; Yip, Calvin K; Burke, John E; Garcia, Christopher K; Grishin, Nick V; Adams, Paul D; Read, Randy J; Baker, David

Accurate prediction of protein structures and interactions using a three-track neural network Journal Article

Science, 2021.

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Koga, Nobuyasu; Koga, Rie; Liu, Gaohua; Castellanos, Javier; Montelione, Gaetano T; Baker, David

Role of backbone strain in de novo design of complex α/β protein structures Journal Article

Nature Communications, 2021.

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Case, James Brett ; Chen, Rita E; Cao, Longxing ; Ying, Baoling ; Winkler, Emma S; Johnson, Max ; Goreshnik, Inna ; Pham, Minh N; Shrihari, Swathi ; Kafai, Natasha M; Bailey, Adam L; Xie, Xuping ; Shi, Pei-Yong ; Ravichandran, Rashmi ; Carter, Lauren ; Stewart, Lance ; Baker, David ; Diamond, Michael S

Ultrapotent miniproteins targeting the SARS-CoV-2 receptor-binding domain protect against infection and disease Journal Article

Cell Host & Microbe, 2021.

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Yaman, Muammer Y; Guye, Kathryn N; Ziatdinov, Maxim; Shen, Hao; Baker, David; Kalinin, Sergei V; Ginger, David S

Alignment of Au nanorods along de novo designed protein nanofibers studied with automated image analysis Journal Article

Soft Matter, 2021.

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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

Proceedings of the National Academy of Sciences, 118 (29), 2021.

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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{"u}ckthun, Andreas ; Wysocki, Vicki H; Veesler, David ; Jensen, Grant J; Baker, David

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

Proceedings of the National Academy of Sciences, 118 (23), 2021.

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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

Nature Communications, 2021.

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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

Proceedings of the National Academy of Sciences, 2021.

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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

Nature Communications, 2021.

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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

Science, 372 (6537), 2021.

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Boyoglu-Barnum, Seyhan ; Ellis, Daniel ; Gillespie, Rebecca A; Hutchinson, Geoffrey B; Park, Young-Jun ; Moin, Syed M; Acton, Oliver J; Ravichandran, Rashmi ; Murphy, Mike ; Pettie, Deleah ; Matheson, Nick ; Carter, Lauren ; Creanga, Adrian ; Watson, Michael J; Kephart, Sally ; Ataca, Sila ; Vaile, John R; Ueda, George ; Crank, Michelle C; Stewart, Lance ; Lee, Kelly K; Guttman, Miklos ; Baker, David ; Mascola, John R; Veesler, David ; Graham, Barney S; King, Neil P; Kanekiyo, Masaru

Quadrivalent influenza nanoparticle vaccines induce broad protection Journal Article

Nature, 2021.

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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, Douglas P; 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

Proceedings of the National Academy of Sciences, 118 (12), 2021.

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Norn, Christoffer ; Wicky, Basile I M; Juergens, David ; Liu, Sirui ; Kim, David ; Tischer, Doug ; Koepnick, Brian ; Anishchenko, Ivan ; Baker, David ; Ovchinnikov, Sergey

Protein sequence design by conformational landscape optimization Journal Article

Proceedings of the National Academy of Sciences, 118 (11), 2021.

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B, Coventry; D, Baker

Protein sequence optimization with a pairwise decomposable penalty for buried unsatisfied hydrogen bonds Journal Article

PLoS Computational Biology, 2021.

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Hiranuma, Naozumi; Park, Hahnbeom; Baek, Minkyung; Anishchenko, Ivan; Dauparas, Justas; Baker, David

Improved protein structure refinement guided by deep learning based accuracy estimation Journal Article

Nature Communications, 12 (1340), 2021.

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Vorobieva, Anastassia A; White, Paul ; Liang, Binyong ; Horne, Jim E; Bera, Asim K; Chow, Cameron M; Gerben, Stacey ; Marx, Sinduja ; Kang, Alex ; Stiving, Alyssa Q; Harvey, Sophie R; Marx, Dagan C; Khan, Nasir G; Fleming, Karen G; Wysocki, Vicki H; Brockwell, David J; Tamm, Lukas K; Radford, Sheena E; Baker, David

De novo design of transmembrane beta barrels Journal Article

Science, 371 (6531), 2021.

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Park, Hahnbeom; Zhou, Guangfeng; Baek, Minkyung; Baker, David; DiMaio, Frank

Force Field Optimization Guided by Small Molecule Crystal Lattice Data Enables Consistent Sub-Angstrom Protein–Ligand Docking Journal Article

Journal of Chemical Theory and Computation, 2021.

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Klima, Jason C; Doyle, Lindsey A; Lee, Justin Daho ; Rappleye, Michael ; Gagnon, Lauren A; Lee, Min Yen ; Barros, Emilia P; Vorobieva, Anastassia A; Dou, Jiayi ; Bremner, Samantha ; Quon, Jacob S; Chow, Cameron M; Carter, Lauren ; Mack, David L; Amaro, Rommie E; Vaughan, Joshua C; Berndt, Andre ; Stoddard, Barry L; Baker, David

Incorporation of sensing modalities into de novo designed fluorescence-activating proteins Journal Article

Nature Communications, 856 (12), pp. 2041–1723, 2021.

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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

Nature, 2021.

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Ziatdinov, Maxim ; Zhang, Shuai ; Dollar, Orion ; Pfaendtner, Jim ; Mundy, Christopher J; Li, Xin ; Pyles, Harley ; Baker, David ; De Yoreo, James J; Kalinin, Sergei V

Quantifying the Dynamics of Protein Self-Organization Using Deep Learning Analysis of Atomic Force Microscopy Data Journal Article

Nano Letters, 2021.

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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

Nature, 2021.

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2020

Caldwell, Shane J; Haydon, Ian C; Piperidou, Nikoletta ; Huang, Po-Ssu ; Bick, Matthew J; Sjöström, Sebastian H; Hilvert, Donald ; Baker, David ; Zeymer, Cathleen

Tight and specific lanthanide binding in a de novo TIM barrel with a large internal cavity designed by symmetric domain fusion Journal Article

Proceedings of the National Academy of Sciences, 2020.

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Mulligan, Vikram Khipple; Kang, Christine S; Sawaya, Michael R; Rettie, Stephen; Li, Xinting; Antselovich, Inna; Craven, Timothy W; Watkins, Andrew M; Labonte, Jason W; DiMaio, Frank; Yeates, Todd O; Baker, David

Computational design of mixed chirality peptide macrocycles with internal symmetry Journal Article

Protein Science, 2020.

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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

Science, 2020.

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Xu, Chunfu; Lu, Peilong; El-Din, Tamer Gamal M; Pei, Xue Y; Johnson, Matthew C; Uyeda, Atsuko; Bick, Matthew J; Xu, Qi; Jiang, Daohua; Bai, Hua; Reggiano, Gabriella; Hsia, Yang; Brunette, T J; Dou, Jiayi; Ma, Dan; Lynch, Eric M; Boyken, Scott E; Huang, Po-Ssu; Stewart, Lance; DiMaio, Frank; Kollman, Justin M; Luisi, Ben F; Matsuura, Tomoaki; Catterall, William A; Baker, David

Computational design of transmembrane pores Journal Article

Nature, 585 , pp. 129–134, 2020.

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Lajoie, Marc J; Boyken, Scott E; Salter, Alexander I; Bruffey, Jilliane ; Rajan, Anusha ; Langan, Robert A; Olshefsky, Audrey ; Muhunthan, Vishaka ; Bick, Matthew J; Gewe, Mesfin ; Quijano-Rubio, Alfredo ; Johnson, JayLee ; Lenz, Garreck ; Nguyen, Alisha ; Pun, Suzie ; Correnti, Colin E; Riddell, Stanley R; Baker, David

Designed protein logic to target cells with precise combinations of surface antigens Journal Article

Science, 2020.

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Kirkpatrick, Robin L; Lewis, Kieran; Langan, Robert A; Lajoie, Marc J; Boyken, Scott E; Eakman, Madeleine; Baker, David; Zalatan, Jesse G

Conditional Recruitment to a DNA-Bound CRISPR–Cas Complex Using a Colocalization-Dependent Protein Switch Journal Article

ACS Synthetic Biology, 2020.

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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

Proceedings of the National Academy of Sciences, 117 (36), pp. 22135–22145, 2020, ISBN: 0027-8424.

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Ueda, George ; Antanasijevic, Aleksandar ; Fallas, Jorge A; Sheffler, William ; Copps, Jeffrey ; Ellis, Daniel ; Hutchinson, Geoffrey B; Moyer, Adam ; Yasmeen, Anila ; Tsybovsky, Yaroslav ; Park, Young-Jun ; Bick, Matthew J; Sankaran, Banumathi ; Gillespie, Rebecca A; Brouwer, Philip JM ; Zwart, Peter H; Veesler, David ; Kanekiyo, Masaru ; Graham, Barney S; Sanders, Rogier W; Moore, John P; Klasse, Per Johan ; Ward, Andrew B; King, Neil P; Baker, David

Tailored design of protein nanoparticle scaffolds for multivalent presentation of viral glycoprotein antigens Journal Article

eLife, 9 , pp. e57659, 2020.

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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

Proceedings of the National Academy of Sciences, 2020.

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Wei, Kathy Y; Moschidi, Danai ; Bick, Matthew J; Nerli, Santrupti ; McShan, Andrew C; Carter, Lauren P; Huang, Po-Ssu ; Fletcher, Daniel A; Sgourakis, Nikolaos G; Boyken, Scott E; Baker, David

Computational design of closely related proteins that adopt two well-defined but structurally divergent folds Journal Article

Proceedings of the National Academy of Sciences, 2020.

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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

Science, 368 (6486), pp. 78-84, 2020.

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Yang, Jianyi ; Anishchenko, Ivan ; Park, Hahnbeom ; Peng, Zhenling ; Ovchinnikov, Sergey ; Baker, David

Improved protein structure prediction using predicted interresidue orientations Journal Article

Proceedings of the National Academy of Sciences, 2020, ISBN: 0027-8424.

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2019

Park, Jooyoung ; Selvaraj, Brinda ; McShan, Andrew C; Boyken, Scott E; Wei, Kathy Y; Oberdorfer, Gustav ; DeGrado, William ; Sgourakis, Nikolaos G; Cuneo, Matthew J; Myles, Dean AA ; Baker, David

De novo design of a homo-trimeric amantadine-binding protein Journal Article

eLife, 2019.

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

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

Protein Science, 2019.

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Foight, Glenna Wink ; Wang, Zhizhi ; Wei, Cindy T; Jr Greisen, Per ; Warner, Katrina M; Cunningham-Bryant, Daniel ; Park, Keunwan ; Brunette, T J; Sheffler, William ; Baker, David ; Maly, Dustin J

Multi-input chemical control of protein dimerization for programming graded cellular responses Journal Article

Nature Biotechnology, 37 (10), pp. 1209-1216, 2019, ISBN: 1546-1696.

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Langan, Robert A; Boyken, Scott E; Ng, Andrew H; Samson, Jennifer A; Dods, Galen ; Westbrook, Alexandra M; Nguyen, Taylor H; Lajoie, Marc J; Chen, Zibo ; Berger, Stephanie ; Mulligan, Vikram Khipple ; Dueber, John E; Novak, Walter R P; El-Samad, Hana ; Baker, David

De novo design of bioactive protein switches Journal Article

Nature, 2019.

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Ng, Andrew H; Nguyen, Taylor H; Gómez-Schiavon, Mariana ; Dods, Galen ; Langan, Robert A; Boyken, Scott E; Samson, Jennifer A; Waldburger, Lucas M; Dueber, John E; Baker, David ; El-Samad, Hana

Modular and tunable biological feedback control using a de novo protein switch Journal Article

Nature, 2019.

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Park, Hahnbeom; Lee, Gyu Rie; Kim, David E; Anishchanka, Ivan; Cong, Qian; Baker, David

High‐accuracy refinement using Rosetta in CASP13 Journal Article

Proteins, 2019.

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Cong, Qian; Anishchenko, Ivan; Ovchinnikov, Sergey; Baker, David

Protein interaction networks revealed by proteome coevolution Journal Article

Science, 2019.

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

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

Nature, 2019.

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Wu, Qi; Peng, Zhenling; Anishchenko, Ivan; Cong, Qian; Baker, David; Yang, Jianyi

Protein contact prediction using metagenome sequence data and residual neural networks Journal Article

Bioinformatics, 36 (1), 2019.

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Koepnick, Brian ; Flatten, Jeff ; Husain, Tamir ; Ford, Alex ; Silva, Daniel-Adriano ; Bick, Matthew J; Bauer, Aaron ; Liu, Gaohua ; Ishida, Yojiro ; Boykov, Alexander ; Estep, Roger D; Kleinfelter, Susan ; Nørgård-Solano, Toke ; Wei, Linda ; Players, Foldit ; Montelione, Gaetano T; DiMaio, Frank ; Popović, Zoran ; Khatib, Firas ; Cooper, Seth ; Baker, David

De novo protein design by citizen scientists Journal Article

Nature, 2019.

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Mohan, Kritika ; Ueda, George ; Kim, Ah Ram ; Jude, Kevin M; Fallas, Jorge A; Guo, Yu ; Hafer, Maximillian ; Miao, Yi ; Saxton, Robert A; Piehler, Jacob ; Sankaran, Vijay G; Baker, David ; Garcia, Christopher K

Topological control of cytokine receptor signaling induces differential effects in hematopoiesis Journal Article

Science, 364 (6442), 2019.

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Boyken, Scott E; Benhaim, Mark A; Busch, Florian ; Jia, Mengxuan ; Bick, Matthew J; Choi, Heejun ; Klima, Jason C; Chen, Zibo ; Walkey, Carl ; Mileant, Alexander ; Sahasrabuddhe, Aniruddha ; Wei, Kathy Y; Hodge, Edgar A; Byron, Sarah ; Quijano-Rubio, Alfredo ; Sankaran, Banumathi ; King, Neil P; Lippincott-Schwartz, Jennifer ; Wysocki, Vicki H; Lee, Kelly K; Baker, David

De novo design of tunable, pH-driven conformational changes Journal Article

Science, 364 (6441), pp. 658-664, 2019.

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Dang, Luke T; Miao, Yi ; Ha, Andrew ; Yuki, Kanako ; Park, Keunwan ; Janda, Claudia Y; Jude, Kevin M; Mohan, Kritika ; Ha, Nhi ; Vallon, Mario ; Yuan, Jenny ; Vilches-Moure, José G; Kuo, Calvin J; Garcia, Christopher K; Baker, David

Receptor subtype discrimination using extensive shape complementary designed interfaces Journal Article

Nature Structural & Molecular Biology, 2019, ISSN: 1545-9985.

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Chen, Zibo ; Johnson, Matthew C; Chen, Jiajun ; Bick, Matthew J; Boyken, Scott E; Lin, Baihan ; De Yoreo, James J; Kollman, Justin M; Baker, David ; DiMaio, Frank

Self-Assembling 2D Arrays with de Novo Protein Building Blocks Journal Article

Journal of the American Chemical Society, 2019.

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de van der Jessica Marcandalli Brooke Fiala, Sebastian Ols Michela Perotti Willem Schueren Joost Snijder Edgar Hodge Mark Benhaim Rashmi Ravichandran Lauren Carter Will Sheffler Livia Brunner Maria Lawrenz Patrice Dubois Antonio Lanzavecchia Federica Sallusto Kelly Lee David Veesler Colin Correnti Lance Stewart David Baker Karin Loré Laurent Perez Neil King K E J P

Induction of Potent Neutralizing Antibody Responses by a Designed Protein Nanoparticle Vaccine for Respiratory Syncytial Virus Journal Article

Cell, 176 (6), pp. 1420-1431, 2019.

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500 entries « 1 of 10 »