Publications

Preprints are available on bioRxiv.

 

2022

FROM THE LAB

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

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

In: Nature Biotechnology, 2022.

Abstract | Links

Computational design of mechanically coupled axle-rotor protein assemblies Journal Article

A. Courbet, J. Hansen, Y. Hsia, N. Bethel, Y.-J. Park, C. Xu, A. Moyer, S. E. Boyken, G. Ueda, U. Nattermann, D. Nagarajan, D. Silva, W. Sheffler, J. Quispe, A. Nord, N. King, P. Bradley, D. Veesler, J. Kollman, D. Baker

In: Science, 2022.

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

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

In: Science Translational Medicine, 2022.

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Design of protein binding proteins from target structure alone Journal Article

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

In: Nature, 2022.

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Generation of Potent and Stable GLP-1 Analogues Via “Serine Ligation” Journal Article

Levine, Paul M., Craven, Timothy W., Li, Xinting, Balana, Aaron T., Bird, Gregory H., Godes, Marina, Salveson, Patrick J., Erickson, Patrick W., Lamb, Mila, Ahlrichs, Maggie, Murphy, Michael, Ogohara, Cassandra, Said, Meerit Y., Walensky, Loren D., Pratt, Matthew R., Baker, David

In: ACS Chemical Biology, 2022.

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Deep learning and protein structure modeling Journal Article

Minkyung Baek, David Baker

In: Nature Methods, 2022.

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Reconfigurable asymmetric protein assemblies through implicit negative design Journal Article

Danny D. Sahtoe, Florian Praetorius, Alexis Courbet, Yang Hsia, Basile I. M. Wicky, Natasha I. Edman, Lauren M. Miller, Bart J. R. Timmermans, Justin Decarreau, Hana M. Morris, Alex Kang, Asim K. Bera, David Baker

In: Science, 2022.

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COLLABORATOR LED

De novo design and directed folding of disulfide-bridged peptide heterodimers Journal Article

Yao, Sicong, Moyer, Adam, Zheng, Yiwu, Shen, Yang, Meng, Xiaoting, Yuan, Chong, Zhao, Yibing, Yao, Hongwei, Baker, David, Wu, Chuanliu

In: Nature Communications, 2022.

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Large-scale design and refinement of stable proteins using sequence-only models Journal Article

Singer, Jedediah M., Novotney, Scott, Strickland, Devin, Haddox, Hugh K., Leiby, Nicholas, Rocklin, Gabriel J., Chow, Cameron M., Roy, Anindya, Bera, Asim K., Motta, Francis C., Cao, Longxing, Strauch, Eva-Maria, Chidyausiku, Tamuka M., Ford, Alex, Ho, Ethan, Zaitzeff, Alexander, Mackenzie, Craig O., Eramian, Hamed, DiMaio, Frank, Grigoryan, Gevorg, Vaughn, Matthew, Stewart, Lance J., Baker, David, Klavins, Eric

In: PLoS ONE, 2022.

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

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

In: Cell Reports, 2022.

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Natural and Designed Proteins Inspired by Extremotolerant Organisms Can Form Condensates and Attenuate Apoptosis in Human Cells Journal Article

Mike T. Veling, Dan T. Nguyen, Nicole N. Thadani, Michela E. Oster, Nathan J. Rollins, Kelly P. Brock, Neville P. Bethel, Samuel Lim, David Baker, Jeffrey C. Way, Debora S. Marks, Roger L. Chang, and Pamela A. Silver

In: ACS Synthetic Biology, 2022.

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Competitive Displacement of De Novo Designed HeteroDimers Can Reversibly Control Protein–Protein Interactions and Implement Feedback in Synthetic Circuits Journal Article

Taylor H. Nguyen, Galen Dods, Mariana Gomez-Schiavon, Muziyue Wu, Zibo Chen, Ryan Kibler, David Baker, Hana El-Samad, Andrew H. Ng

In: GEN Biotechnology, 2022.

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Interpreting neural networks for biological sequences by learning stochastic masks Journal Article

Linder, Johannes, La Fleur, Alyssa, Chen, Zibo, Ljubetič, Ajasja, Baker, David, Kannan, Sreeram, Seelig, Georg

In: Nature Machine Intelligence, 2022.

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

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

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

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2021

FROM THE LAB

De novo protein design by deep network hallucination Journal Article

Anishchenko, Ivan and Pellock, Samuel J. and Chidyausiku, Tamuka M. and Ramelot, Theresa A. and Ovchinnikov, Sergey and Hao, Jingzhou and Bafna, Khushboo and Norn, Christoffer and Kang, Alex and Bera, Asim K. and DiMaio, Frank and Carter, Lauren and Chow, Cameron M. and Montelione, Gaetano T. and Baker, David

In: Nature, 2021.

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Computed structures of core eukaryotic protein complexes Journal Article

Ian R. Humphreys, Jimin Pei, Minkyung Baek, Aditya Krishnakumar, Ivan Anishchenko, Sergey Ovchinnikov, Jing Zhang, Travis J. Ness, Sudeep Banjade, Saket R. Bagde, Viktoriya G. Stancheva, Xiao-Han Li, Kaixian Liu, Zhi Zheng, Daniel J. Barrero, Upasana Roy, Jochen Kuper, Israel S. Fernández, Barnabas Szakal, Dana Branzei, Josep Rizo, Caroline Kisker, Eric C. Greene, Sue Biggins, Scott Keeney, Elizabeth A. Miller, J. Christopher Fromme, Tamara L. Hendrickson, Qian Cong, David Baker

In: Science, 2021.

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

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

In: Nature Structural & Molecular Biology, 2021.

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

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

In: Proteins, 2021.

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

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

In: Science, 2021.

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

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

In: Nature Communications, 2021.

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

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

In: Cell Host & Microbe, 2021.

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Computational design of a synthetic PD-1 agonist Journal Article

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

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

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

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"uckthun, Andreas, Wysocki, Vicki H., Veesler, David, Jensen, Grant J., Baker, David

In: Proceedings of the National Academy of Sciences, vol. 118, no. 23, 2021.

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

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

In: Nature Communications, 2021.

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Transferrin receptor targeting by de novo sheet extension Journal Article

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

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

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Design of multi-scale protein complexes by hierarchical building block fusion Journal Article

Hsia, Yang and Mout, Rubul and Sheffler, William and Edman, Natasha I. and Vulovic, Ivan and Park, Young-Jun and Redler, Rachel L. and Bick, Matthew J. and Bera, Asim K. and Courbet, Alexis and Kang, Alex and Brunette, T. J. and Nattermann, Una and Tsai, Evelyn and Saleem, Ayesha and Chow, Cameron M. and Ekiert, Damian and Bhabha, Gira and Veesler, David and Baker, David

In: Nature Communications, 2021.

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Designed proteins assemble antibodies into modular nanocages Journal Article

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

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

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

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

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

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Protein sequence design by conformational landscape optimization Journal Article

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

In: Proceedings of the National Academy of Sciences, vol. 118, no. 11, 2021.

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

Coventry B, Baker D

In: PLoS Computational Biology, 2021.

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De novo design of transmembrane beta barrels Journal Article

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, G. Nasir, Fleming, Karen G., Wysocki, Vicki H., Brockwell, David J., Tamm, Lukas K., Radford, Sheena E., Baker, David

In: Science, vol. 371, no. 6531, 2021.

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

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

In: Nature Communications, vol. 856, no. 12, pp. 2041–1723, 2021.

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De novo design of modular and tunable protein biosensors Journal Article

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

In: Nature, 2021.

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Design of biologically active binary protein 2D materials Journal Article

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

In: Nature, 2021.

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COLLABORATOR LED

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

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.

In: Nature Chemistry, 2021.

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

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

In: Science Translational Medicine, 2021.

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The trRosetta server for fast and accurate protein structure prediction Journal Article

Du, Zongyang and Su, Hong and Wang, Wenkai and Ye, Lisha and Wei, Hong and Peng, Zhenling and Anishchenko, Ivan and Baker, David and Yang, Jianyi

In: Nature Protocols, 2021.

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

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

In: Soft Matter, 2021.

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Quadrivalent influenza nanoparticle vaccines induce broad protection Journal Article

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

In: Nature, 2021.

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

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

In: Nature Communications, vol. 12, no. 1340, 2021.

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

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

In: Journal of Chemical Theory and Computation, 2021.

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

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

In: Nano Letters, 2021.

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2020

FROM THE LAB

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

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

In: Protein Science, 2020.

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

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

In: Science, 2020.

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Computational design of transmembrane pores Journal Article

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

In: Nature, vol. 585, pp. 129–134, 2020.

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

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

In: Science, 2020.

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

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

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

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

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

In: eLife, vol. 9, pp. e57659, 2020.

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Modular repeat protein sculpting using rigid helical junctions Journal Article

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

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

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

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

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

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De novo design of protein logic gates Journal Article

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

In: Science, vol. 368, no. 6486, pp. 78-84, 2020.

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Improved protein structure prediction using predicted interresidue orientations Journal Article

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

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

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COLLABORATOR LED

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

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

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

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

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

In: ACS Synthetic Biology, 2020.

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2019

FROM THE LAB

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

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

In: eLife, 2019.

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

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

In: Protein Science, 2019.

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De novo design of bioactive protein switches Journal Article

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

In: Nature, 2019.

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

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

In: Nature, 2019.

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High‐accuracy refinement using Rosetta in CASP13 Journal Article

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

In: Proteins, 2019.

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Protein interaction networks revealed by proteome coevolution Journal Article

Qian Cong, Ivan Anishchenko, Sergey Ovchinnikov, David Baker

In: Science, 2019.

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

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

In: Nature, 2019.

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De novo protein design by citizen scientists Journal Article

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

In: Nature, 2019.

Links

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

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

In: Science, vol. 364, no. 6441, pp. 658-664, 2019.

Abstract | Links

Receptor subtype discrimination using extensive shape complementary designed interfaces Journal Article

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, K. Christopher, Baker, David

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

Links

What has de novo protein design taught us about protein folding and biophysics? Journal Article

David Baker

In: Protein Science, vol. 28, no. 4, pp. 678-683, 2019.

Abstract | Links

De novo design of potent and selective mimics of IL-2 and IL-15 Journal Article

Silva, Daniel-Adriano and Yu, Shawn and Ulge, Umut Y. and Spangler, Jamie B. and Jude, Kevin M. and Labão-Almeida, Carlos and Ali, Lestat R. and Quijano-Rubio, Alfredo and Ruterbusch, Mikel and Leung, Isabel and Biary, Tamara and Crowley, Stephanie J. and Marcos, Enrique and Walkey, Carl D. and Weitzner, Brian D. and Pardo-Avila, Fátima and Castellanos, Javier and Carter, Lauren and Stewart, Lance and Riddell, Stanley R. and Pepper, Marion and Bernardes, Gonçalo J. L. and Dougan, Michael and Garcia, K. Christopher and Baker, David

In: Nature, 2019, ISSN: 1476-4687.

Abstract | Links

COLLABORATOR LED

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

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.

In: Nature Biotechnology, vol. 37, no. 10, pp. 1209-1216, 2019, ISBN: 1546-1696.

Abstract | Links

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

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

In: Bioinformatics, vol. 36, no. 1, 2019.

Abstract | Links

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

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, K. Christopher

In: Science, vol. 364, no. 6442, 2019.

Abstract | Links

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

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

In: Journal of the American Chemical Society, 2019.

Abstract | Links

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

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

In: Cell, vol. 176, no. 6, pp. 1420-1431, 2019.

Abstract | Links

2018

FROM THE LAB

Programmable design of orthogonal protein heterodimers Journal Article

Chen, Zibo and Boyken, Scott E. and Jia, Mengxuan and Busch, Florian and Flores-Solis, David and Bick, Matthew J. and Lu, Peilong and VanAernum, Zachary L. and Sahasrabuddhe, Aniruddha and Langan, Robert A. and Bermeo, Sherry and Brunette, T. J. and Mulligan, Vikram Khipple and Carter, Lauren P. and DiMaio, Frank and Sgourakis, Nikolaos G. and Wysocki, Vicki H. and Baker, David

In: Nature, 2018, ISSN: 1476-4687.

Abstract | Links

De novo design of self-assembling helical protein filaments Journal Article

Shen, Hao, Fallas, Jorge A., Lynch, Eric, Sheffler, William, Parry, Bradley, Jannetty, Nicholas, Decarreau, Justin, Wagenbach, Michael, Vicente, Juan Jesus, Chen, Jiajun, Wang, Lei, Dowling, Quinton, Oberdorfer, Gustav, Stewart, Lance, Wordeman, Linda, De Yoreo, James, Jacobs-Wagner, Christine, Kollman, Justin, Baker, David

In: Science, vol. 362, no. 6415, pp. 705–709, 2018, ISSN: 0036-8075.

Abstract | Links

De novo design of a non-local β-sheet protein with high stability and accuracy Journal Article

Marcos, Enrique and Chidyausiku, Tamuka M. and McShan, Andrew C. and Evangelidis, Thomas and Nerli, Santrupti and Carter, Lauren and Nivón, Lucas G. and Davis, Audrey and Oberdorfer, Gustav and Tripsianes, Konstantinos and Sgourakis, Nikolaos G. and Baker, David

In: Nature Structural & Molecular Biology, 2018, ISSN: 1545-9985.

Abstract | Links

De novo design of a fluorescence-activating β-barrel Journal Article

Jiayi Dou*, Anastassia A. Vorobieva*, William Sheffler, Lindsey A. Doyle, Hahnbeom Park, Matthew J. Bick, Binchen Mao, Glenna W. Foight, Min Yen Lee, Lauren A. Gagnon, Lauren Carter, Banumathi Sankaran, Sergey Ovchinnikov, Enrique Marcos, Po-Ssu Huang, Joshua C. Vaughan, Barry L. Stoddard, David Baker

In: Nature, 2018, ISSN: 1476-4687.

Abstract | Links

Protein homology model refinement by large-scale energy optimization Journal Article

Park, Hahnbeom, Ovchinnikov, Sergey, Kim, David E., DiMaio, Frank, Baker, David

In: Proceedings of the National Academy of Sciences, vol. 115, no. 12, pp. 3054–3059, 2018, ISSN: 0027-8424.

Abstract | Links

Accurate computational design of multipass transmembrane proteins Journal Article

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

In: Science, vol. 359, no. 6379, pp. 1042–1046, 2018, ISSN: 0036-8075.

Abstract | Links

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

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

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

Abstract | Links

COLLABORATOR LED

Unintended specificity of an engineered ligand-binding protein facilitated by unpredicted plasticity of the protein fold Journal Article

Day, Austin L, Greisen, Per, Doyle, Lindsey, Schena, Alberto, Stella, Nephi, Johnsson, Kai, Baker, David, Stoddard, Barry

In: Protein Engineering, Design and Selection, 2018.

Abstract | Links

Simple yet functional phosphate-loop proteins Journal Article

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.

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

Abstract | Links

Extreme stability in de novo-designed repeat arrays is determined by unusually stable short-range interactions Journal Article

Geiger-Schuller, Kathryn, Sforza, Kevin, Yuhas, Max, Parmeggiani, Fabio, Baker, David, Barrick, Doug

In: PNAS, vol. 115, no. 29, pp. 7539-7544, 2018, ISSN: 0027-8424.

Abstract | Links

Discovery and engineering of enhanced SUMO protease enzymes Journal Article

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

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

Abstract | Links

2017–1998

ALL PAPERS
437 entries « 1 of 15 »

2017

Comprehensive computational design of ordered peptide macrocycles Journal Article

Hosseinzadeh, Parisa*, Bhardwaj, Gaurav*, Mulligan, Vikram Khipple*, Shortridge, Matthew D., Craven, Timothy W., Pardo-Avila, F'atima, Rettie, Stephen A., Kim, David E., Silva, Daniel-Adriano, Ibrahim, Yehia M., Webb, Ian K., Cort, John R., Adkins, Joshua N., Varani, Gabriele, Baker, David

In: Science, vol. 358, no. 6369, pp. 1461-1466, 2017, ISSN: 0036-8075.

Abstract | Links

Evolution of a designed protein assembly encapsulating its own RNA genome Journal Article

Butterfield, Gabriel L.* and Lajoie, Marc J.* and Gustafson, Heather H. and Sellers, Drew L. and Nattermann, Una and Ellis, Daniel and Bale, Jacob B. and Ke, Sharon and Lenz, Garreck H. and Yehdego, Angelica and Ravichandran, Rashmi and Pun, Suzie H. and King, Neil P. and Baker, David

In: Nature, 2017, ISSN: 1476-4687.

Abstract | Links

Sampling and energy evaluation challenges in ligand binding protein design Journal Article

Jiayi Dou, Lindsey Doyle, Per Greisen, Alberto Schena, Hahnbeom Park, Kai Johnsson, Barry Stoddard, David Baker

In: Protein Science, vol. 26, pp. 2426-2437, 2017, ISSN: 1469-896.

Abstract | Links

Massively parallel de novo protein design for targeted therapeutics Journal Article

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

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

Abstract | Links

Protein structure prediction using Rosetta in CASP12 Journal Article

Sergey Ovchinnikov, Hahnbeom Park, David E. Kim, Frank DiMaio, David Baker

In: Proteins, 2017.

Abstract | Links

Computational design of environmental sensors for the potent opioid fentanyl Journal Article

Bick, Matthew J*, Greisen, Per J*, Morey, Kevin J, Antunes, Mauricio S, La, David, Sankaran, Banumathi, Reymond, Luc, Johnsson, Kai, Medford, June I, Baker, David

In: eLife Sciences Publications, vol. 6, pp. e28909, 2017, ISBN: 2050-084X.

Abstract | Links

Origins of coevolution between residues distant in protein 3D structures Journal Article

I Anishchenko, S Ovchinnikov, H Kamisetty, D Baker

In: Proceedings of the National Academy of Sciences, vol. 114, no. 34, pp. 9122-9127, 2017.

Abstract | Links

Cyclic oligomer design with de novo αβ-proteins Journal Article

Yu-Ru Lin, Nobuyasu Koga, Sergey M. Vorobiev, David Baker

In: Protein Science, 2017.

Abstract | Links

Global analysis of protein folding using massively parallel design, synthesis, and testing Journal Article

GJ Rocklin, TM Chidyausiku, I Goreshnik, A Ford, S Houliston, A Lemak, L Carter, R Ravichandran, VK Mulligan, A Chevalier, CH Arrowsmith, D Baker

In: Science, vol. 357, pp. 168-175, 2017.

Abstract | Links

Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site Journal Article

Strauch, Eva-Maria, Bernard, Steffen M, La, David, Bohn, Alan J, Lee, Peter S, Anderson, Caitlin E, Nieusma, Travis, Holstein, Carly A, Garcia, Natalie K, Hooper, Kathryn A, Ravichandran, Rashmi, Nelson, Jorgen W, Sheffler, William, Bloom, Jesse D, Lee, Kelly K, Ward, Andrew B, Yager, Paul, Fuller, Deborah H, Wilson, Ian A, Baker, David

In: Nature Biotechnology, vol. [Epub ahead of print], 2017, ISSN: 1546-1696.

Abstract | Links

Surrogate Wnt agonists that phenocopy canonical Wnt and β-catenin signalling. Journal Article

Janda CY, Dang LT, You C, Chang J, de Lau W, Zhong ZA, Yan KS, Marecic O, Siepe D, Li X, Moody JD, Williams BO, Clevers H, Piehler J, Baker D, Kuo CJ, Garcia KC

In: Nature, vol. 545, no. 7653, pp. 234-237, 2017.

Abstract | Links

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

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

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

Abstract | Links

Protein structure determination using metagenome sequence data Journal Article

Sergey Ovchinnikov, Hahnbeom Park, Neha Varghese, Po-Ssu Huang, Georgios A. Pavlopoulos, David E. Kim, Hetunandan Kamisetty, Nikos C. Kyrpides, David Baker

In: Science, vol. 355, no. 6322, pp. 294–298, 2017, ISSN: 0036-8075.

Abstract | Links

2016

Computational design of a homotrimeric metalloprotein with a trisbipyridyl core Journal Article

Jeremy H. Mills, William Sheffler, Maraia E. Ener, Patrick J. Almhjell, Gustav Oberdorfer, José Henrique Pereira, Fabio Parmeggiani, Banumathi Sankaran, Peter H. Zwart, David Baker

In: PNAS, vol. 113, no. 52, pp. 15012-15017, 2016.

Abstract | Links

Computational design of self-assembling cyclic protein homo-oligomers Journal Article

Fallas JA, Ueda G, Sheffler W, Nguyen V, McNamara DE, Sankaran B, Pereira JH, Parmeggiani F, Brunette TJ, Cascio D, Yeates TR, Zwart P, Baker D

In: Nature Chemistry, vol. 9, pp. 353–360, 2016.

Abstract | Links

Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer Journal Article

Stephanie Berger, Erik Procko, Daciana Margineantu, Erinna F Lee, Betty W Shen, Alex Zelter, Daniel-Adriano Silva, and Kusum Chawla, Marco J Herold, Jean-Marc Garnier, Richard Johnson, Michael J MacCoss, Guillaume Lessene, Trisha N Davis, Patrick S Stayton, Barry L Stoddard, W Douglas Fairlie, David M Hockenbery, David Baker

In: Elife, 2016.

Abstract | Links

The coming of age of de novo protein design Journal Article

Po-Ssu Huang, Scott E. Boyken, David Baker

In: Nature, vol. 537, pp. 320-327, 2016.

Abstract | Links

Accurate de novo design of hyperstable constrained peptides Journal Article

Gaurav Bhardwaj*, Vikram Khipple Mulligan*, Christopher D. Bahl*, Jason M. Gilmore, Peta J. Harvey, Olivier Cheneval, Garry W. Buchko, Surya V. S. R. K. Pulavarti, Quentin Kaas, Alexander Eletsky, Po-Ssu Huang, William A. Johnsen, Per Jr Greisen, Gabriel J. Rocklin, Yifan Song, Thomas W. Linsky, Andrew Watkins, Stephen A. Rettie, Xianzhong Xu, Lauren P. Carter, Richard Bonneau, James M. Olson, Evangelos Coutsias, Colin E. Correnti, Thomas Szyperski, David J. Craik, David Baker

In: Nature, 2016.

Abstract | Links

Accurate design of megadalton-scale two-component icosahedral protein complexes Journal Article

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

In: Science, vol. 353, no. 6297, pp. 389-394, 2016.

Abstract | Links

Design of a hyperstable 60-subunit protein icosahedron Journal Article

Yang Hsia*, Jacob B. Bale*, Shane Gonen, Dan Shi, William Sheffler, Kimberly K. Fong, Nattermann, Chunfu Xu, Po-Ssu Huang, Rashmi Ravichandran, Sue Yi, Trisha N. Davis, Tamir Gonen, Neil P. King, David Baker

In: Nature, 2016.

Abstract | Links

Multiplex pairwise assembly of array-derived DNA oligonucleotides Journal Article

Klein, J. C., Lajoie, M. J., Schwartz, J. J., Strauch, E.-M., Nelson, J., Baker, D., & Shendure, J

In: Nucleic Acids Research, vol. 44, no. 5, pp. e43, 2016.

Abstract | Links

Engineering an allosteric transcription factor to respond to new ligands Journal Article

Taylor ND, Garruss AS, Moretti R, Chan S, Arbing MA, Cascio D, Rogers JK, Isaacs FJ, Kosuri S, Baker D, Fields S, Church GM, Raman S

In: Nature Methods, vol. 13, no. 2, pp. 177-83, 2016.

Abstract | Links

De novo design of protein homo-oligomers with modular hydrogen-bond network–mediated specificity Journal Article

Scott E. Boyken, Zibo Chen, Benjamin Groves, Robert A. Langan, Gustav Oberdorfer, Alex Ford, Jason M. Gilmore, Chunfu Xu, Frank DiMaio, Jose Henrique Pereira, Banumathi Sankaran, Georg Seelig, Peter H. Zwart, David Baker

In: Science, vol. 352, no. 6286, pp. 680–687, 2016, ISSN: 0036-8075.

Abstract | Links

Structure prediction using sparse simulated NOE restraints with Rosetta in CASP11 Journal Article

Ovchinnikov, Sergey, Park, Hahnbeom, Kim, David E., Liu, Yuan, Wang, Ray Yu-Ruei, Baker, David

In: Proteins: Structure, Function, and Bioinformatics, pp. n/a–n/a, 2016, ISSN: 1097-0134.

Abstract | Links

Introduction of a polar core into the de novo designed protein Top7 Journal Article

Benjamin Basanta, Kui K. Chan, Patrick Barth, Tiffany King, Tobin R. Sosnick, James R. Hinshaw, Gaohua Liu, John K. Everett, Rong Xiao, Gaetano T. Montelione, David Baker

In: Protein Science, pp. n/a–n/a, 2016, ISSN: 1469-896X.

Abstract | Links

A Computationally Designed Hemagglutinin Stem-Binding Protein Provides In Vivo Protection from Influenza Independent of a Host Immune Response Journal Article

Merika Treants AND Nelson Jorgen AND Chevalier Aaron AND Koday Michael AND Kalinoski Hannah AND Stewart Lance AND Carter Lauren AND Nieusma Travis AND Lee Peter S. AND Ward Andrew B. AND Wilson Ian A. AND Dagley Ashley AND Smee Donald F. AND Baker David AND Fuller Deborah Heydenburg Koday

In: PLoS Pathog, vol. 12, no. 2, pp. 1-23, 2016.

Abstract | Links

Designed protein aggregates entrapping carbon nanotubes for bioelectrochemical oxygen reduction Journal Article

Kristen E Garcia, Sofia Babanova, William Scheffler, Mansij Hans, David Baker, Plamen Atanassov, Scott Banta

In: Biotechnology and Bioengineering, pp. n/a–n/a, 2016, ISSN: 1097-0290.

Abstract | Links

2015

A general strategy to construct small molecule biosensors in eukaryotes Journal Article

J Feng, BW Jester, CE Tinberg, DJ Mandell, MS Antunes, R Chari, KJ Morey, X Rios, JI Medford, GM Church, S Fields, D Baker

In: Elife, 2015.

Abstract | Links

Rational design of α-helical tandem repeat proteins with closed architectures Journal Article

L Doyle, J Hallinan, J Bolduc, F Parmeggiani, D Baker, BL Stoddard, P Bradley

In: Nature, vol. 528(7583), pp. 585-8, 2015.

Abstract | Links

Exploring the repeat protein universe through computational protein design Journal Article

TJ Brunette, F Parmeggiani, PS Huang, G Bhabha, DC Ekiert, SE Tsutakawa, GL Hura, JA Tainer, D Baker

In: Nature, vol. 528(7583), pp. 580-4, 2015.

Abstract | Links

437 entries « 1 of 15 »