Publications

Preprints are available on bioRxiv.

 

2022

FROM THE LAB

B. I. M. Wicky, L. F. Milles, A. Courbet, R. J. Ragotte, J. Dauparas, E. Kinfu, S. Tipps, R. D. Kibler, M. Baek, F. DiMaio, X. Li, L. Carter, A. Kang, H. Nguyen, A. K. Bera, D. Baker

Hallucinating symmetric protein assemblies Journal Article

In: Science, 2022.

Abstract | Links

Dauparas, J. and Anishchenko, I. and Bennett, N. and Bai, H. and Ragotte, R. J. and Milles, L. F. and Wicky, B. I. M. and Courbet, A. and de Haas, R. J. and Bethel, N. and Leung, P. J. Y. and Huddy, T. F. and Pellock, S. and Tischer, D. and Chan, F. and Koepnick, B. and Nguyen, H. and Kang, A. and Sankaran, B. and Bera, A. K. and King, N. P. and Baker, D.

Robust deep learning–based protein sequence design using ProteinMPNN Journal Article

In: Science, 2022.

Abstract | Links

Gaurav Bhardwaj, Jacob O’Connor, Stephen Rettie, Yen-Hua Huang, Theresa A. Ramelot, Vikram Khipple Mulligan, Gizem Gokce Alpkilic, Jonathan Palmer, Asim K. Bera, Matthew J. Bick, Maddalena Di Piazza, Xinting Li, Parisa Hosseinzadeh, Timothy W. Craven, Roberto Tejero, Anna Lauko, Ryan Choi, Calina Glynn, Linlin Dong, Robert Griffin, Wesley C. van Voorhis, Jose Rodriguez, Lance Stewart, Gaetano T. Montelione, David Craik, David Baker

Accurate de novo design of membrane-traversing macrocycles Bachelor Thesis

2022.

Abstract | Links

Yang, Erin C. and Divine, Robby and Kang, Christine S. and Chan, Sidney and Arenas, Elijah and Subol, Zoe and Tinker, Peter and Manninen, Hayden and Feichtenbiner, Alicia and Mustafa, Talal and Hallowell, Julia and Orr, Isiac and Haddox, Hugh and Koepnick, Brian and O’Connor, Jacob and Haydon, Ian C. and Herpoldt, Karla-Luise and Wormer, Kandise Van and Abell, Celine and Baker, David and Khmelinskaia, Alena and King, Neil P.

Increasing Computational Protein Design Literacy through Cohort-Based Learning for Undergraduate Students Journal Article

In: Journal of Chemical Education, 2022.

Abstract | Links

Derrick R. Hicks, Madison A. Kennedy, Kirsten A. Thompson, Michelle DeWitt, Brian Coventry, Alex Kang, Asim K. Bera, T. J. Brunette, Banumathi Sankaran, Barry Stoddard, David Baker

De novo design of protein homodimers containing tunable symmetric protein pockets Journal Article

In: Proceedings of the National Academy of Sciences, 2022.

Abstract | Links

Jue Wang, Sidney Lisanza, David Juergens, Doug Tischer, Joseph L. Watson, Karla M. Castro, Robert Ragotte, Amijai Saragovi, Lukas F. Milles, Minkyung Baek, Ivan Anishchenko, Wei Yang, Derrick R. Hicks, Marc Expòsit, Thomas Schlichthaerle, Jung-Ho Chun, Justas Dauparas, Nathaniel Bennett, Basile I. M. Wicky, Andrew Muenks, Frank DiMaio, Bruno Correia, Sergey Ovchinnikov, David Baker

Scaffolding protein functional sites using deep learning Journal Article

In: Science, 2022.

Abstract | Links

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

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

In: Nature Biotechnology, 2022.

Abstract | Links

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

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

In: Science, 2022.

Abstract | Links

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

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

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

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

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

In: ACS Chemical Biology, 2022.

Abstract | Links

Minkyung Baek, David Baker

Deep learning and protein structure modeling Journal Article

In: Nature Methods, 2022.

Abstract | Links

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

Reconfigurable asymmetric protein assemblies through implicit negative design Journal Article

In: Science, 2022.

Abstract | Links

COLLABORATOR LED

Sen, Neeladri and Anishchenko, Ivan and Bordin N and Sillitoe, Ian and Velankar, Sameer and Baker, David and Orengo, Christine

Characterizing and explaining the impact of disease-associated mutations in proteins without known structures or structural homologs Journal Article

In: Briefings in Bioinformatics, 2022.

Abstract | Links

Macé, Kévin and Vadakkepat, Abhinav K. and Redzej, Adam and Lukoyanova, Natalya and Oomen, Clasien and Braun, Nathalie and Ukleja, Marta and Lu, Fang and Costa, Tiago R. D. and Orlova, Elena V. and Baker, David and Cong, Qian and Waksman, Gabriel

Cryo-EM structure of a type IV secretion system Bachelor Thesis

2022.

Abstract | Links

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

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

2022.

Abstract | Links

Sarah L. Lovelock, Rebecca Crawshaw, Sophie Basler, Colin Levy, David Baker, Donald Hilvert, Anthony P. Green

The road to fully programmable protein catalysis Journal Article

In: Nature, 2022.

Abstract | Links

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

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

In: Nature Communications, 2022.

Abstract | Links

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

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

In: PLoS ONE, 2022.

Abstract | Links

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

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

In: Cell Reports, 2022.

Abstract | Links

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

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

In: ACS Synthetic Biology, 2022.

Abstract | Links

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

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

In: GEN Biotechnology, 2022.

Abstract | Links

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

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

In: Nature Machine Intelligence, 2022.

Abstract | Links

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

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

2021

FROM THE LAB

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

De novo protein design by deep network hallucination Journal Article

In: Nature, 2021.

Abstract | Links

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

Computed structures of core eukaryotic protein complexes Journal Article

In: Science, 2021.

Abstract | Links

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

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

In: Nature Structural & Molecular Biology, 2021.

Abstract | Links

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

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

In: Proteins, 2021.

Abstract | Links

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

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

In: Science, 2021.

Abstract | Links

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

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

In: Nature Communications, 2021.

Abstract | Links

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.

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

In: Cell Host & Microbe, 2021.

Abstract | Links

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

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

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

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

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

Abstract | Links

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

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

In: Nature Communications, 2021.

Abstract | Links

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

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

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

In: Nature Communications, 2021.

Abstract | Links

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

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

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

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

Abstract | Links

Coventry B, Baker D

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

In: PLoS Computational Biology, 2021.

Abstract | Links

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

De novo design of transmembrane beta barrels Journal Article

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

Abstract | Links

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

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

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

Abstract | Links

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

De novo design of modular and tunable protein biosensors Journal Article

In: Nature, 2021.

Abstract | Links

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

In: Nature, 2021.

Abstract | Links

COLLABORATOR LED

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.

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

In: Nature Chemistry, 2021.

Abstract | Links

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

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

In: Science Translational Medicine, 2021.

Abstract | Links

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

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

In: Nature Protocols, 2021.

Abstract | Links

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

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

In: Soft Matter, 2021.

Abstract | Links

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

Quadrivalent influenza nanoparticle vaccines induce broad protection Journal Article

In: Nature, 2021.

Abstract | Links

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

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

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

Abstract | Links

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

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

In: Journal of Chemical Theory and Computation, 2021.

Abstract | Links

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.

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

In: Nano Letters, 2021.

Abstract | Links

2020

FROM THE LAB

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

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

In: Protein Science, 2020.

Abstract | Links

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

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

Computational design of transmembrane pores Journal Article

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

Abstract | Links

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

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

In: Science, 2020.

Abstract | Links

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

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

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

Abstract | Links

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

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

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

Abstract | Links

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

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

Improved protein structure prediction using predicted interresidue orientations Journal Article

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

Abstract | Links

COLLABORATOR LED

Caldwell, Shane J., Haydon, Ian C., Piperidou, Nikoletta, Huang, Po-Ssu, Bick, Matthew J., Sjöström, H. Sebastian, 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

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

Abstract | Links

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

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

In: ACS Synthetic Biology, 2020.

Abstract | Links

2019

FROM THE LAB

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

In: eLife, 2019.

Abstract | Links

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

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

In: Protein Science, 2019.

Abstract | Links

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

In: Nature, 2019.

Abstract | Links

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

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

In: Nature, 2019.

Abstract | Links

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

High‐accuracy refinement using Rosetta in CASP13 Journal Article

In: Proteins, 2019.

Abstract | Links

Qian Cong, Ivan Anishchenko, Sergey Ovchinnikov, David Baker

Protein interaction networks revealed by proteome coevolution Journal Article

In: Science, 2019.

Abstract | Links

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

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

In: Nature, 2019.

Abstract | Links

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

De novo protein design by citizen scientists Journal Article

In: Nature, 2019.

Links

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

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

Abstract | Links

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

Receptor subtype discrimination using extensive shape complementary designed interfaces Journal Article

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

Links

David Baker

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

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

Abstract | Links

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

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

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

Abstract | Links

COLLABORATOR LED

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

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

Abstract | Links

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

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

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

Abstract | Links

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

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

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

Abstract | Links

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

In: Journal of the American Chemical Society, 2019.

Abstract | Links

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,

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

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

Abstract | Links

2018

FROM THE LAB

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

Programmable design of orthogonal protein heterodimers Journal Article

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

Abstract | Links

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

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

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

Abstract | Links

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

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

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

Abstract | Links

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

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

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

Abstract | Links

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

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

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

Abstract | Links

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

Accurate computational design of multipass transmembrane proteins Journal Article

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

Abstract | Links

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

COLLABORATOR LED

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

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

In: Protein Engineering, Design and Selection, 2018.

Abstract | Links

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

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

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

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

Abstract | Links

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

Discovery and engineering of enhanced SUMO protease enzymes Journal Article

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

Abstract | Links

2017–1998

ALL PAPERS
437 entries « 1 of 15 »

2017

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

Comprehensive computational design of ordered peptide macrocycles Journal Article

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

Abstract | Links

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

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

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

Abstract | Links

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

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

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

Abstract | Links

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

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

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

Protein structure prediction using Rosetta in CASP12 Journal Article

In: Proteins, 2017.

Abstract | Links

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

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

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

Abstract | Links

I Anishchenko, S Ovchinnikov, H Kamisetty, D Baker

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

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

Abstract | Links

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

Cyclic oligomer design with de novo αβ-proteins Journal Article

In: Protein Science, 2017.

Abstract | Links

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

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

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

Abstract | Links

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

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

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

Abstract | Links

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

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

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

Abstract | Links

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

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

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

Abstract | Links

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

Protein structure determination using metagenome sequence data Journal Article

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

Abstract | Links

2016

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

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

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

Abstract | Links

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

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

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

Abstract | Links

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

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

In: Elife, 2016.

Abstract | Links

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

The coming of age of de novo protein design Journal Article

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

Abstract | Links

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

Accurate de novo design of hyperstable constrained peptides Journal Article

In: Nature, 2016.

Abstract | Links

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

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

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

Abstract | Links

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

Design of a hyperstable 60-subunit protein icosahedron Journal Article

In: Nature, 2016.

Abstract | Links

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

Multiplex pairwise assembly of array-derived DNA oligonucleotides Journal Article

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

Abstract | Links

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

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

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

Abstract | Links

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

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

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

Abstract | Links

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

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

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

Abstract | Links

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

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

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

Abstract | Links

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

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

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

Abstract | Links

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

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

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

Abstract | Links

2015

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

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

In: Elife, 2015.

Abstract | Links

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

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

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

Abstract | Links

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

Exploring the repeat protein universe through computational protein design Journal Article

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

Abstract | Links

437 entries « 1 of 15 »