Julien S Baker (D Baker, David Baker)

ResearcherID ORCID

Publication Activity (10 Years)

Years Active: 2016-2023
Publications (10 Years): 162

Top Venues

Proceedings of the National Academy of Sciences of the United States of America

Science (New York, N.Y.)

Nature communications

Nature

University of Washington Howard Hughes Medical Institute

University of California Berkeley (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

University of Washington Howard Hughes Medical Institute

United States

Investigator

Education History

University of California Berkeley

United States

PHD :: Biochemistry

Publications

Amir Motmaen, Justas Dauparas, Minkyung Baek, Mohamad H Abedi, Julien S Baker, Philip G Bradley
Peptide-binding specificity prediction using fine-tuned protein structure prediction networks. Proceedings of the National Academy of Sciences of the United States of America 120 (9) (2023)
David E Kim, Davin R Jensen, David Feldman, Doug Tischer, Ayesha Saleem, Cameron M Chow, Xinting Li, Lauren Carter, Lukas F Milles, Hannah Nguyen, Alex Kang, Asim K Bera, Francis C Peterson, Brian F Volkman, Sergey Ovchinnikov, Julien S Baker
De novo design of small beta barrel proteins. Proceedings of the National Academy of Sciences of the United States of America 120 (11) (2023)
Joseph L Watson, David Juergens, Nathaniel R Bennett, Brian L Trippe, Jason Yim, Helen E Eisenach, Woody Ahern, Andrew J Borst, Robert J Ragotte, Lukas F Milles, Basile I M Wicky, Nikita Hanikel, Samuel J Pellock, Alexis Courbet, William Sheffler, Jue Wang, Preetham Venkatesh, Isaac Sappington, Susana Vázquez Torres, Anna Lauko, Valentin De Bortoli, Emile Mathieu, Sergey Ovchinnikov, Regina Barzilay, Tommi S Jaakkola, Frank DiMaio, Minkyung Baek, Julien S Baker
De novo design of protein structure and function with RFdiffusion. Nature (2023)
Sanaa Mansoor, Minkyung Baek, David Juergens, Joseph L Watson, Julien S Baker
Zero-shot Mutation Effect Prediction on Protein Stability and Function using RoseTTAFold. Protein science : a publication of the Protein Society (2023)
Edin Muratspahić, Kristine Deibler, Jianming Han, Nataša Tomašević, Kirtikumar B Jadhav, Aina-Leonor Olivé-Marti, Nadine Hochrainer, Roland Hellinger, Johannes Koehbach, Jonathan F Fay, Mohammad Homaidur Rahman, Lamees Hegazy, Timothy W Craven, Balazs R Varga, Gaurav Bhardwaj, Kevin Appourchaux, Susruta Majumdar, Markus Muttenthaler, Parisa Hosseinzadeh, David J Craik, Mariana Spetea, Tao Che, Julien S Baker, Christian W Gruber
Design and structural validation of peptide-drug conjugate ligands of the kappa-opioid receptor. Nature communications 14 (1) (2023)
Robbert J de Haas, Natalie Brunette, Alex Goodson, Justas Dauparas, Sue Y Yi, Erin C Yang, Quinton Dowling, Hannah Nguyen, Alex Kang, Asim K Bera, Banumathi Sankaran, Renko de Vries, Julien S Baker, Neil P King
Rapid and automated design of two-component protein nanomaterials using ProteinMPNN. bioRxiv : the preprint server for biology (2023)
Eliza S Nieweglowska, Axel F Brilot, Melissa Mèndez-Moran, Claire Kokontis, Minkyung Baek, Junrui Li, Yifan Cheng, Julien S Baker, Joseph Bondy-Denomy, David A Agard
The ϕPA3 phage nucleus is enclosed by a self-assembling 2D crystalline lattice. Nature communications 14 (1) (2023)
Nathan M Ennist, Shunzhi Wang, Madison Kennedy, Mariano Curti, George Sutherland, Cvetelin Vasilev, Rachel Redler, Valentin Maffeis, Saeed Shareef, Anthony Sica, Ash Hua, Arundhati Deshmukh, Adam Moyer, Derrick Hicks, Avi Swartz, Ralph Cacho, Nathan Novy, Asim K Bera, Alex Kang, Banumathi Sankaran, Matthew Johnson, Mike Reppert, Damian C Ekiert, Gira Bhabha, Lance J Stewart, Justin Caram, Barry L Stoddard, Elisabet Romero, Christopher Neil Hunter, Julien S Baker
De novo design of energy transfer proteins housing excitonically coupled chlorophyll special pairs. Research square (2023)
Isaac D Lutz, Shunzhi Wang, Christoffer H Norn, Alexis Courbet, Andrew J Borst, Yan Ting Zhao, Annie M Dosey, Longxing Cao, Jinwei Xu, Elizabeth M Leaf, Catherine Treichel, Patrisia Litvicov, Zhe Li, Alexander D Goodson, Paula Rivera-Sánchez, Ana-Maria Bratovianu, Minkyung Baek, Neil P King, Hannele Ruohola-Baker, Julien S Baker
Top-down design of protein architectures with reinforcement learning. Science (New York, N.Y.) 380 (6642) (2023)
Enrico Rennella, Danny D Sahtoe, Julien S Baker, Lewis E Kay
Exploiting conformational dynamics to modulate the function of designed proteins. Proceedings of the National Academy of Sciences of the United States of America 120 (18) (2023)
Georgios A Pavlopoulos, Fotis A Baltoumas, Sirui Liu, Oguz Selvitopi, Antonio Pedro Camargo, Stephen Nayfach, Ariful Azad, Simon Roux, Lee Call, Natalia N Ivanova, I Min Chen, A David Páez-Espino, Evangelos Karatzas, null null, Ioannis Iliopoulos, Konstantinos T Konstantinidis, James M Tiedje, Jennifer Pett-Ridge, Julien S Baker, Axel Visel, Christos A Ouzounis, Sergey Ovchinnikov, Aydin Buluç, Nikos C Kyrpides
Unraveling the functional dark matter through global metagenomics. Nature (2023)
Erin C Yang, Robby Divine, Marcos C Miranda, Andrew J Borst, William Sheffler, Jason Z Zhang, Justin Decarreau, Amijai Saragovi, Mohamad H Abedi, Nicolas Goldbach, Maggie Ahlrichs, Craig Dobbins, Alexis Hand, Suna Cheng, Mila Lamb, Paul M Levine, Sidney Chan, Rebecca Skotheim, Jorge Fallas, George Ueda, Joshua M Lubner, Masaharu Somiya, Alena Khmelinskaia, Neil P King, Julien S Baker
Computational design of non-porous, pH-responsive antibody nanoparticles. bioRxiv : the preprint server for biology (2023)
Andy Hsien-Wei Yeh, Christoffer H Norn, Yakov Kipnis, Doug K Tischer, Samuel J Pellock, Declan Evans, Pengchen Ma, Gyu Rie Lee, Jason Z Zhang, Ivan Anishchenko, Brian Coventry, Longxing Cao, Justas Dauparas, Samer Halabiya, Michelle DeWitt, Lauren Carter, Kendall N Houk, Julien S Baker
De novo design of luciferases using deep learning. Nature 614 (7949) (2023)
Hanlun Jiang, Kevin M Jude, Kejia Wu, Jorge Fallas, George Ueda, T J Brunette, Derrick R Hicks, Harley Pyles, Aerin Yang, Lauren Carter, Mila Lamb, Xinting Li, Paul M Levine, Lance Stewart, K Christopher Garcia, Julien S Baker
De novo design of buttressed loops for sculpting protein functions. bioRxiv : the preprint server for biology (2023)
Zhe Li, Shunzhi Wang, Una Nattermann, Asim K Bera, Andrew J Borst, Muammer Y Yaman, Matthew J Bick, Erin C Yang, William Sheffler, Byeongdu Lee, Soenke Seifert, Greg L Hura, Hannah Nguyen, Alex Kang, Radhika Dalal, Joshua M Lubner, Yang Hsia, Hugh Haddox, Alexis Courbet, Quinton Dowling, Marcos C Miranda, Andrew Favor, Ali Etemadi, Natasha I Edman, Wei Yang, Connor Weidle, Banumathi Sankaran, Babak Negahdari, Michael B Ross, David S Ginger, Julien S Baker
Accurate computational design of three-dimensional protein crystals. Nature materials (2023)
David E Kim, Davin R Jensen, David Feldman, Doug Tischer, Ayesha Saleem, Cameron M Chow, Xinting Li, Lauren Carter, Lukas F Milles, Hannah Nguyen, Alex Kang, Asim K Bera, Francis C Peterson, Brian F Volkman, Sergey Ovchinnikov, Julien S Baker
De novo design of small beta barrel proteins. Proceedings of the National Academy of Sciences of the United States of America 120 (11) (2023)
Eliza S Nieweglowska, Axel F Brilot, Melissa Mèndez-Moran, Claire Kokontis, Minkyung Baek, Junrui Li, Yifan Cheng, Julien S Baker, Joseph Bondy-Denomy, David A Agard
The ϕPA3 phage nucleus is enclosed by a self-assembling 2D crystalline lattice. Nature communications 14 (1) (2023)
David E Kim, Davin R Jensen, David Feldman, Doug Tischer, Ayesha Saleem, Cameron M Chow, Xinting Li, Lauren Carter, Lukas F Milles, Hannah Nguyen, Alex Kang, Asim K Bera, Francis C Peterson, Brian F Volkman, Sergey Ovchinnikov, Julien S Baker
De novo design of small beta barrel proteins. Proceedings of the National Academy of Sciences of the United States of America 120 (11) (2023)
Andy Hsien-Wei Yeh, Christoffer H Norn, Yakov Kipnis, Doug K Tischer, Samuel J Pellock, Declan Evans, Pengchen Ma, Gyu Rie Lee, Jason Z Zhang, Ivan Anishchenko, Brian Coventry, Longxing Cao, Justas Dauparas, Samer Halabiya, Michelle DeWitt, Lauren Carter, Kendall N Houk, Julien S Baker
De novo design of luciferases using deep learning. Nature 614 (7949) (2023)
Isaac D Lutz, Shunzhi Wang, Christoffer H Norn, Alexis Courbet, Andrew J Borst, Yan Ting Zhao, Annie M Dosey, Longxing Cao, Jinwei Xu, Elizabeth M Leaf, Catherine Treichel, Patrisia Litvicov, Zhe Li, Alexander D Goodson, Paula Rivera-Sánchez, Ana-Maria Bratovianu, Minkyung Baek, Neil P King, Hannele Ruohola-Baker, Julien S Baker
Top-down design of protein architectures with reinforcement learning. Science (New York, N.Y.) 380 (6642) (2023)
Andy Hsien-Wei Yeh, Christoffer H Norn, Yakov Kipnis, Doug K Tischer, Samuel J Pellock, Declan Evans, Pengchen Ma, Gyu Rie Lee, Jason Z Zhang, Ivan Anishchenko, Brian Coventry, Longxing Cao, Justas Dauparas, Samer Halabiya, Michelle DeWitt, Lauren Carter, Kendall N Houk, Julien S Baker
De novo design of luciferases using deep learning. Nature 614 (7949) (2023)
Geoffrey B Hutchinson, Olubukola M Abiona, Cynthia T Ziwawo, Anne P Werner, Daniel Ellis, Yaroslav Tsybovsky, Sarah R Leist, Charis Palandjian, Ande West, Ethan J Fritch, Nianshuang Wang, Daniel Wrapp, Seyhan Boyoglu-Barnum, George Ueda, Julien S Baker, Masaru Kanekiyo, Jason S Mclellan, Ralph S Baric, Neil P King, Barney S Graham, Kizzmekia S Corbett-Helaire
Nanoparticle display of prefusion coronavirus spike elicits S1-focused cross-reactive antibody response against diverse coronavirus subgenera. Nature communications 14 (1) (2023)
Andy Hsien-Wei Yeh, Christoffer H Norn, Yakov Kipnis, Doug K Tischer, Samuel J Pellock, Declan Evans, Pengchen Ma, Gyu Rie Lee, Jason Z Zhang, Ivan Anishchenko, Brian Coventry, Longxing Cao, Justas Dauparas, Samer Halabiya, Michelle DeWitt, Lauren Carter, Kendall N Houk, Julien S Baker
De novo design of luciferases using deep learning. Nature 614 (7949) (2023)
Enrico Rennella, Danny D Sahtoe, Julien S Baker, Lewis E Kay
Exploiting conformational dynamics to modulate the function of designed proteins. Proceedings of the National Academy of Sciences of the United States of America 120 (18) (2023)
Audrey Olshefsky, Halli Benasutti, Meilyn Sylvestre, Gabriel L Butterfield, Gabriel J Rocklin, Christian Richardson, Derrick R Hicks, Marc J Lajoie, Kefan Song, Elizabeth M Leaf, Catherine Treichel, Justin Decarreau, Sharon Ke, Gargi Kher, Lauren Carter, Jeffrey S Chamberlain, Julien S Baker, Neil P King, Suzie H Pun
In vivo selection of synthetic nucleocapsids for tissue targeting. Proceedings of the National Academy of Sciences of the United States of America 120 (46) (2023)
Nathaniel R Bennett, Brian Coventry, Inna Goreshnik, Buwei Huang, Aza Allen, Dionne Vafeados, Ying Po Peng, Justas Dauparas, Minkyung Baek, Lance J Stewart, Frank DiMaio, Steven De Munck, Savvas N Savvides, Julien S Baker
Improving de novo protein binder design with deep learning. Nature communications 14 (1) (2023)
Jason Z Zhang, Nathan Greenwood, Jason Hernandez, Josh T Cuperus, Buwei Huang, Bryan D Ryder, Christine Queitsch, Jason E Gestwicki, Julien S Baker
De novo designed Hsp70 activator dissolves intracellular condensates. bioRxiv : the preprint server for biology (2023)
Nicolas Goldbach, Issa Benna, Basile I M Wicky, Jacob T Croft, Lauren Carter, Asim K Bera, Hannah Nguyen, Alex Kang, Banumathi Sankaran, Erin C Yang, Kelly K Lee, Julien S Baker
De novo design of monomeric helical bundles for pH-controlled membrane lysis. Protein science : a publication of the Protein Society (2023)
Jason Z Zhang, Shao-En Ong, Julien S Baker, Dustin J Maly
Single-cell signaling analysis reveals that Major Vault Protein facilitates RasG12C inhibitor resistance. bioRxiv : the preprint server for biology (2023)
Minkyung Baek, Ryan McHugh, Ivan Anishchenko, Hanlun Jiang, Julien S Baker, Frank DiMaio
Accurate prediction of protein-nucleic acid complexes using RoseTTAFoldNA. Nature methods (2023)
Eliza S Nieweglowska, Axel F Brilot, Melissa Mèndez-Moran, Claire Kokontis, Minkyung Baek, Junrui Li, Yifan Cheng, Julien S Baker, Joseph Bondy-Denomy, David A Agard
The ϕPA3 phage nucleus is enclosed by a self-assembling 2D crystalline lattice. Nature communications 14 (1) (2023)
Kejia Wu, Hua Bai, Ya-Ting Chang, Rachel Redler, Kerrie E McNally, William Sheffler, T J Brunette, Derrick R Hicks, Tomos E Morgan, Tim J Stevens, Adam Broerman, Inna Goreshnik, Michelle DeWitt, Cameron M Chow, Yihang Shen, Lance J Stewart, Emmanuel Derivery, Daniel Adriano Silva, Gira Bhabha, Damian C Ekiert, Julien S Baker
De novo design of modular peptide-binding proteins by superhelical matching. Nature (2023)
Jing Yang John Wang, Alena Khmelinskaia, William Sheffler, Marcos C Miranda, Aleksandar Antanasijevic, Andrew J Borst, Susana V Torres, Chelsea Shu, Yang Hsia, Una Nattermann, Daniel Ellis, Carl Walkey, Maggie Ahlrichs, Sidney Chan, Alex Kang, Hannah Nguyen, Claire Sydeman, Banumathi Sankaran, Mengyu Wu, Asim K Bera, Lauren Carter, Brooke Fiala, Michael Murphy, Julien S Baker, Andrew B Ward, Neil P King
Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains. Proceedings of the National Academy of Sciences of the United States of America 120 (11) (2023)
Enrico Rennella, Danny D Sahtoe, Julien S Baker, Lewis E Kay
Exploiting conformational dynamics to modulate the function of designed proteins. Proceedings of the National Academy of Sciences of the United States of America 120 (18) (2023)
Jing Yang John Wang, Alena Khmelinskaia, William Sheffler, Marcos C Miranda, Aleksandar Antanasijevic, Andrew J Borst, Susana V Torres, Chelsea Shu, Yang Hsia, Una Nattermann, Daniel Ellis, Carl Walkey, Maggie Ahlrichs, Sidney Chan, Alex Kang, Hannah Nguyen, Claire Sydeman, Banumathi Sankaran, Mengyu Wu, Asim K Bera, Lauren Carter, Brooke Fiala, Michael Murphy, Julien S Baker, Andrew B Ward, Neil P King
Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains. Proceedings of the National Academy of Sciences of the United States of America 120 (11) (2023)
Jing Yang John Wang, Alena Khmelinskaia, William Sheffler, Marcos C Miranda, Aleksandar Antanasijevic, Andrew J Borst, Susana V Torres, Chelsea Shu, Yang Hsia, Una Nattermann, Daniel Ellis, Carl Walkey, Maggie Ahlrichs, Sidney Chan, Alex Kang, Hannah Nguyen, Claire Sydeman, Banumathi Sankaran, Mengyu Wu, Asim K Bera, Lauren Carter, Brooke Fiala, Michael Murphy, Julien S Baker, Andrew B Ward, Neil P King
Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains. Proceedings of the National Academy of Sciences of the United States of America 120 (11) (2023)
Nathan M Ennist, Shunzhi Wang, Madison Kennedy, Mariano Curti, George Sutherland, Cvetelin Vasilev, Rachel Redler, Valentin Maffeis, Saeed Shareef, Anthony Sica, Ash Hua, Arundhati Deshmukh, Adam Moyer, Derrick Hicks, Avi Swartz, Ralph Cacho, Nathan Novy, Asim K Bera, Alex Kang, Banumathi Sankaran, Matthew Johnson, Mike Reppert, Damian C Ekiert, Gira Bhabha, Lance J Stewart, Justin Caram, Barry L Stoddard, Elisabet Romero, Christopher Neil Hunter, Julien S Baker
De novo design of energy transfer proteins housing excitonically coupled chlorophyll special pairs. Research square (2023)
William Sheffler, Erin C Yang, Quinton Dowling, Yang Hsia, Chelsea N Fries, Jenna Stanislaw, Mark D Langowski, Marisa Brandys, Zhe Li, Rebecca Skotheim, Andrew J Borst, Alena Khmelinskaia, Neil P King, Julien S Baker
Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock. PLoS computational biology 19 (5) (2023)
Jing Yang John Wang, Alena Khmelinskaia, William Sheffler, Marcos C Miranda, Aleksandar Antanasijevic, Andrew J Borst, Susana V Torres, Chelsea Shu, Yang Hsia, Una Nattermann, Daniel Ellis, Carl Walkey, Maggie Ahlrichs, Sidney Chan, Alex Kang, Hannah Nguyen, Claire Sydeman, Banumathi Sankaran, Mengyu Wu, Asim K Bera, Lauren Carter, Brooke Fiala, Michael Murphy, Julien S Baker, Andrew B Ward, Neil P King
Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains. Proceedings of the National Academy of Sciences of the United States of America 120 (11) (2023)
Dingchang Lin, Xiuyuan Li, Eric Moult, Pojeong Park, Benjamin Tang, Hao Shen, Jonathan B Grimm, Natalie Falco, Bill Z Jia, Julien S Baker, Luke D Lavis, Adam E Cohen
Time-tagged ticker tapes for intracellular recordings. Nature biotechnology (2023)
Nathaniel R Bennett, Brian Coventry, Inna Goreshnik, Buwei Huang, Aza Allen, Dionne Vafeados, Ying Po Peng, Justas Dauparas, Minkyung Baek, Lance J Stewart, Frank DiMaio, Steven De Munck, Savvas N Savvides, Julien S Baker
Improving de novo protein binder design with deep learning. Nature communications 14 (1) (2023)
Dingchang Lin, Xiuyuan Li, Eric Moult, Pojeong Park, Benjamin Tang, Hao Shen, Jonathan B Grimm, Natalie Falco, Bill Z Jia, Julien S Baker, Luke D Lavis, Adam E Cohen
Time-tagged ticker tapes for intracellular recordings. Nature biotechnology (2023)
Isaac D Lutz, Shunzhi Wang, Christoffer H Norn, Alexis Courbet, Andrew J Borst, Yan Ting Zhao, Annie M Dosey, Longxing Cao, Jinwei Xu, Elizabeth M Leaf, Catherine Treichel, Patrisia Litvicov, Zhe Li, Alexander D Goodson, Paula Rivera-Sánchez, Ana-Maria Bratovianu, Minkyung Baek, Neil P King, Hannele Ruohola-Baker, Julien S Baker
Top-down design of protein architectures with reinforcement learning. Science (New York, N.Y.) 380 (6642) (2023)
Amir Motmaen, Justas Dauparas, Minkyung Baek, Mohamad H Abedi, Julien S Baker, Philip G Bradley
Peptide-binding specificity prediction using fine-tuned protein structure prediction networks. Proceedings of the National Academy of Sciences of the United States of America 120 (9) (2023)
Ryan D Kibler, Sangmin Lee, Madison A Kennedy, Basile I M Wicky, Stella M Lai, Marius M Kostelic, Xinting Li, Cameron M Chow, Lauren Carter, Vicki H Wysocki, Barry L Stoddard, Julien S Baker
Stepwise design of pseudosymmetric protein hetero-oligomers. bioRxiv : the preprint server for biology (2023)
Enrico Rennella, Danny D Sahtoe, Julien S Baker, Lewis E Kay
Exploiting conformational dynamics to modulate the function of designed proteins. Proceedings of the National Academy of Sciences of the United States of America 120 (18) (2023)
Eliza S Nieweglowska, Axel F Brilot, Melissa Mèndez-Moran, Claire Kokontis, Minkyung Baek, Junrui Li, Yifan Cheng, Julien S Baker, Joseph Bondy-Denomy, David A Agard
The ϕPA3 phage nucleus is enclosed by a self-assembling 2D crystalline lattice. Nature communications 14 (1) (2023)
Enrico Rennella, Danny D Sahtoe, Julien S Baker, Lewis E Kay
Exploiting conformational dynamics to modulate the function of designed proteins. Proceedings of the National Academy of Sciences of the United States of America 120 (18) (2023)
Nathaniel R Bennett, Brian Coventry, Inna Goreshnik, Buwei Huang, Aza Allen, Dionne Vafeados, Ying Po Peng, Justas Dauparas, Minkyung Baek, Lance J Stewart, Frank DiMaio, Steven De Munck, Savvas N Savvides, Julien S Baker
Improving de novo protein binder design with deep learning. Nature communications 14 (1) (2023)
Enrico Rennella, Danny D Sahtoe, Julien S Baker, Lewis E Kay
Exploiting conformational dynamics to modulate the function of designed proteins. Proceedings of the National Academy of Sciences of the United States of America 120 (18) (2023)
Andy Hsien-Wei Yeh, Christoffer H Norn, Yakov Kipnis, Doug K Tischer, Samuel J Pellock, Declan Evans, Pengchen Ma, Gyu Rie Lee, Jason Z Zhang, Ivan Anishchenko, Brian Coventry, Longxing Cao, Justas Dauparas, Samer Halabiya, Michelle DeWitt, Lauren Carter, Kendall N Houk, Julien S Baker
De novo design of luciferases using deep learning. Nature 614 (7949) (2023)
Isaac D Lutz, Shunzhi Wang, Christoffer H Norn, Alexis Courbet, Andrew J Borst, Yan Ting Zhao, Annie M Dosey, Longxing Cao, Jinwei Xu, Elizabeth M Leaf, Catherine Treichel, Patrisia Litvicov, Zhe Li, Alexander D Goodson, Paula Rivera-Sánchez, Ana-Maria Bratovianu, Minkyung Baek, Neil P King, Hannele Ruohola-Baker, Julien S Baker
Top-down design of protein architectures with reinforcement learning. Science (New York, N.Y.) 380 (6642) (2023)
Isaac D Lutz, Shunzhi Wang, Christoffer H Norn, Alexis Courbet, Andrew J Borst, Yan Ting Zhao, Annie M Dosey, Longxing Cao, Jinwei Xu, Elizabeth M Leaf, Catherine Treichel, Patrisia Litvicov, Zhe Li, Alexander D Goodson, Paula Rivera-Sánchez, Ana-Maria Bratovianu, Minkyung Baek, Neil P King, Hannele Ruohola-Baker, Julien S Baker
Top-down design of protein architectures with reinforcement learning. Science (New York, N.Y.) 380 (6642) (2023)
Neville P Bethel, Andrew J Borst, Fabio Parmeggiani, Matthew J Bick, T J Brunette, Hannah Nguyen, Alex Kang, Asim K Bera, Lauren Carter, Marcos C Miranda, Ryan D Kibler, Mila Lamb, Xinting Li, Banumathi Sankaran, Julien S Baker
Precisely patterned nanofibres made from extendable protein multiplexes. Nature chemistry (2023)
Andy Hsien-Wei Yeh, Christoffer H Norn, Yakov Kipnis, Doug K Tischer, Samuel J Pellock, Declan Evans, Pengchen Ma, Gyu Rie Lee, Jason Z Zhang, Ivan Anishchenko, Brian Coventry, Longxing Cao, Justas Dauparas, Samer Halabiya, Michelle DeWitt, Lauren Carter, Kendall N Houk, Julien S Baker
De novo design of luciferases using deep learning. Nature 614 (7949) (2023)
Enrico Rennella, Danny D Sahtoe, Julien S Baker, Lewis E Kay
Exploiting conformational dynamics to modulate the function of designed proteins. Proceedings of the National Academy of Sciences of the United States of America 120 (18) (2023)
Enrico Rennella, Danny D Sahtoe, Julien S Baker, Lewis E Kay
Exploiting conformational dynamics to modulate the function of designed proteins. Proceedings of the National Academy of Sciences of the United States of America 120 (18) (2023)
Anindya Roy, Lei Shi, Ashley Chang, Xianchi Dong, Andres N Fernandez, John C Kraft, Jing Li, Viet Q Le, Rebecca Viazzo Winegar, Gerald Maxwell Cherf, Dean Slocum, Peter Daniel Poulson, Garrett E Casper, Mary L Vallecillo-Zúniga, Jonard Corpuz Valdoz, Marcos C Miranda, Hua Bai, Yakov Kipnis, Audrey Olshefsky, Tanu Priya, Lauren Carter, Rashmi Ravichandran, Cameron M Chow, Max R Johnson, Suna Cheng, McKaela Smith, Catherine Overed-Sayer, Donna K Finch, David Lowe, Asim K Bera, Gustavo Matute-Bello, Timothy P Birkland, Frank DiMaio, Ganesh Raghu, Jennifer R Cochran, Lance J Stewart, Melody G Campbell, Pam M Van Ry, Timothy A Springer, Julien S Baker
De novo design of highly selective miniprotein inhibitors of integrins αvβ6 and αvβ8. Nature communications 14 (1) (2023)
Isaac D Lutz, Shunzhi Wang, Christoffer H Norn, Alexis Courbet, Andrew J Borst, Yan Ting Zhao, Annie M Dosey, Longxing Cao, Jinwei Xu, Elizabeth M Leaf, Catherine Treichel, Patrisia Litvicov, Zhe Li, Alexander D Goodson, Paula Rivera-Sánchez, Ana-Maria Bratovianu, Minkyung Baek, Neil P King, Hannele Ruohola-Baker, Julien S Baker
Top-down design of protein architectures with reinforcement learning. Science (New York, N.Y.) 380 (6642) (2023)
Florian Praetorius, Philip J Y Leung, Maxx H Tessmer, Adam Broerman, Cullen Demakis, Acacia F Dishman, Arvind S Pillai, Abbas Idris, David C Juergens, Justas Dauparas, Xinting Li, Paul M Levine, Mila Lamb, Ryanne K Ballard, Stacey R Gerben, Hannah Nguyen, Alex Kang, Banumathi Sankaran, Asim K Bera, Brian F Volkman, Jeff Nivala, Stefan Stoll, Julien S Baker
Design of stimulus-responsive two-state hinge proteins. Science (New York, N.Y.) 381 (6659) (2023)
Nathan M Ennist, Shunzhi Wang, Madison Kennedy, Mariano Curti, George Sutherland, Cvetelin Vasilev, Rachel Redler, Valentin Maffeis, Saeed Shareef, Anthony Sica, Ash Hua, Arundhati Deshmukh, Adam Moyer, Derrick Hicks, Avi Swartz, Ralph Cacho, Nathan Novy, Asim K Bera, Alex Kang, Banumathi Sankaran, Matthew Johnson, Mike Reppert, Damian C Ekiert, Gira Bhabha, Lance J Stewart, Justin Caram, Barry L Stoddard, Elisabet Romero, Christopher Neil Hunter, Julien S Baker
De novo design of energy transfer proteins housing excitonically coupled chlorophyll special pairs. Research square (2023)
Linna An, Derrick R Hicks, Dmitri Zorine, Justas Dauparas, Basile I M Wicky, Lukas F Milles, Alexis Courbet, Asim K Bera, Hannah Nguyen, Alex Kang, Lauren Carter, Julien S Baker
Hallucination of closed repeat proteins containing central pockets. Nature structural & molecular biology (2023)
Amir Motmaen, Justas Dauparas, Minkyung Baek, Mohamad H Abedi, Julien S Baker, Philip G Bradley
Peptide-binding specificity prediction using fine-tuned protein structure prediction networks. Proceedings of the National Academy of Sciences of the United States of America 120 (9) (2023)
Amir Motmaen, Justas Dauparas, Minkyung Baek, Mohamad H Abedi, Julien S Baker, Philip G Bradley
Peptide-binding specificity prediction using fine-tuned protein structure prediction networks. Proceedings of the National Academy of Sciences of the United States of America 120 (9) (2023)
Isaac D Lutz, Shunzhi Wang, Christoffer H Norn, Alexis Courbet, Andrew J Borst, Yan Ting Zhao, Annie M Dosey, Longxing Cao, Jinwei Xu, Elizabeth M Leaf, Catherine Treichel, Patrisia Litvicov, Zhe Li, Alexander D Goodson, Paula Rivera-Sánchez, Ana-Maria Bratovianu, Minkyung Baek, Neil P King, Hannele Ruohola-Baker, Julien S Baker
Top-down design of protein architectures with reinforcement learning. Science (New York, N.Y.) 380 (6642) (2023)
Julien S Baker, Quinton Dowling, Young-Jun Park, Neil Gerstenmaier, Erin Yang, Adam Wargacki, Yang Hsia, Chelsea Fries, Rashmi Ravichandran, Carl Walkey, Anika Burrell, David J Veesler, Neil P King
Hierarchical design of pseudosymmetric protein nanoparticles. Research square (2023)
Nathaniel R Bennett, Brian Coventry, Inna Goreshnik, Buwei Huang, Aza Allen, Dionne Vafeados, Ying Po Peng, Justas Dauparas, Minkyung Baek, Lance J Stewart, Frank DiMaio, Steven De Munck, Savvas N Savvides, Julien S Baker
Improving de novo protein binder design with deep learning. Nature communications 14 (1) (2023)
Erin C Yang, Robby Divine, Marcos C Miranda, Andrew J Borst, William Sheffler, Jason Z Zhang, Justin Decarreau, Amijai Saragovi, Mohamad H Abedi, Nicolas Goldbach, Maggie Ahlrichs, Craig Dobbins, Alexis Hand, Suna Cheng, Mila Lamb, Paul M Levine, Sidney Chan, Rebecca Skotheim, Jorge Fallas, George Ueda, Joshua M Lubner, Masaharu Somiya, Alena Khmelinskaia, Neil P King, Julien S Baker
Computational design of non-porous, pH-responsive antibody nanoparticles. bioRxiv : the preprint server for biology (2023)
Huilin Yang, Umut Y Ulge, Alfredo Quijano-Rubio, Zachary J Bernstein, David R Maestas, Jung-Ho Chun, Wentao Wang, Jian-Xin Lin, Kevin M Jude, Srujan Singh, Brian T Orcutt-Jahns, Peng Li, Jody Mou, Liam Chung, Yun-Huai Kuo, Yasmin H Ali, Aaron S Meyer, Warren L Grayson, Nicola M Heller, K Christopher Garcia, Warren J Leonard, Daniel Adriano Silva, Jennifer H Elisseeff, Julien S Baker, Jamie B Spangler
Design of cell-type-specific hyperstable IL-4 mimetics via modular de novo scaffolds. Nature chemical biology (2023)
Tamuka M Chidyausiku, Soraia R Mendes, Jason C Klima, Marta Nadal, Ulrich Eckhard, Jorge Roel-Touris, Scott Houliston, Tibisay Guevara, Hugh K Haddox, Adam Moyer, Cheryl H Arrowsmith, Francesc Xavier Gomis-Rüth, Julien S Baker, Enrique Marcos
De novo design of immunoglobulin-like domains. Nature communications 13 (1) (2022)
Shuai Zhang, Robbie Sadre, Benjamin A Legg, Harley Pyles, Talita Perciano Costa Leite, E Wes Bethel, Julien S Baker, Oliver Rübel, James J De Yoreo
Rotational dynamics and transition mechanisms of surface-adsorbed proteins. Proceedings of the National Academy of Sciences of the United States of America 119 (16) (2022)
Sherry Bermeo, Andrew Favor, Ya-Ting Chang, Andrew Norris, Scott E Boyken, Yang Hsia, Hugh K Haddox, Chunfu Xu, T J Brunette, Vicki H Wysocki, Gira Bhabha, Damian C Ekiert, Julien S Baker
De novo design of obligate ABC-type heterotrimeric proteins. Nature structural & molecular biology (2022)
Sherry Bermeo, Andrew Favor, Ya-Ting Chang, Andrew Norris, Scott E Boyken, Yang Hsia, Hugh K Haddox, Chunfu Xu, T J Brunette, Vicki H Wysocki, Gira Bhabha, Damian C Ekiert, Julien S Baker
De novo design of obligate ABC-type heterotrimeric proteins. Nature structural & molecular biology 29 (12) (2022)
Sherry Bermeo, Andrew Favor, Ya-Ting Chang, Andrew Norris, Scott E Boyken, Yang Hsia, Hugh K Haddox, Chunfu Xu, T J Brunette, Vicki H Wysocki, Gira Bhabha, Damian C Ekiert, Julien S Baker
De novo design of obligate ABC-type heterotrimeric proteins. Nature structural & molecular biology 29 (12) (2022)
Alexis Courbet, Jesse M Hansen, Yang Hsia, Neville P Bethel, Young-Jun Park, Chunfu Xu, A Moyer, Scott E Boyken, George Ueda, Una Nattermann, Deepesh Nagarajan, Daniel Adriano Silva, William Sheffler, J Quispe, Ashley L Nord, Neil P King, Philip G Bradley, David J Veesler, Justin M Kollman, Julien S Baker
Computational design of mechanically coupled axle-rotor protein assemblies. Science (New York, N.Y.) 376 (6591) (2022)
Minkyung Baek, Julien S Baker
Deep learning and protein structure modeling. Nature methods 19 (1) (2022)
Sarah L Lovelock, Rebecca Crawshaw, Sophie Basler, Colin Levy, Julien S Baker, Donald Hilvert, Anthony P Green
The road to fully programmable protein catalysis. Nature 606 (7912) (2022)
Sherry Bermeo, Andrew Favor, Ya-Ting Chang, Andrew Norris, Scott E Boyken, Yang Hsia, Hugh K Haddox, Chunfu Xu, T J Brunette, Vicki H Wysocki, Gira Bhabha, Damian C Ekiert, Julien S Baker
De novo design of obligate ABC-type heterotrimeric proteins. Nature structural & molecular biology 29 (12) (2022)
Sherry Bermeo, Andrew Favor, Ya-Ting Chang, Andrew Norris, Scott E Boyken, Yang Hsia, Hugh K Haddox, Chunfu Xu, T J Brunette, Vicki H Wysocki, Gira Bhabha, Damian C Ekiert, Julien S Baker
De novo design of obligate ABC-type heterotrimeric proteins. Nature structural & molecular biology 29 (12) (2022)
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, Julien S Baker
Reconfigurable asymmetric protein assemblies through implicit negative design. Science (New York, N.Y.) 375 (6578) (2022)
Jason Z Zhang, Andy Hsien-Wei Yeh, Alexandra C Walls, Basile I M Wicky, Kaitlin R Sprouse, Laura A VanBlargan, Rebecca Treger, Alfredo Quijano-Rubio, Minh N Pham, John C Kraft, Ian C Haydon, Wei Yang, Michelle DeWitt, John E Bowen, Cameron M Chow, Lauren Carter, Rashmi Ravichandran, Mark H Wener, Lance J Stewart, David J Veesler, Michael S. Diamond, Alexander L Greninger, David M Koelle, Julien S Baker
Thermodynamically coupled biosensors for detecting neutralizing antibodies against SARS-CoV-2 variants. Nature biotechnology 40 (9) (2022)
Andrew C Hunt, James Brett Case, Young-Jun Park, Longxing Cao, Kejia Wu, Alexandra C Walls, Zhuoming Liu, John E Bowen, Andy 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 I 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 J Stewart, Michael S. Diamond, David J Veesler, Michael C Jewett, Julien S Baker
Multivalent designed proteins neutralize SARS-CoV-2 variants of concern and confer protection against infection in mice. Science translational medicine 14 (646) (2022)
Basile I M Wicky, Lukas F Milles, Alexis Courbet, Robert Ragotte, Justas Dauparas, E Kinfu, S Tipps, Ryan D Kibler, Minkyung Baek, Frank DiMaio, Xinting Li, Lauren Carter, Alex Kang, Hannah Nguyen, Asim K Bera, Julien S Baker
Hallucinating symmetric protein assemblies. Science (New York, N.Y.) 378 (6615) (2022)
Sherry Bermeo, Andrew Favor, Ya-Ting Chang, Andrew Norris, Scott E Boyken, Yang Hsia, Hugh K Haddox, Chunfu Xu, T J Brunette, Vicki H Wysocki, Gira Bhabha, Damian C Ekiert, Julien S Baker
De novo design of obligate ABC-type heterotrimeric proteins. Nature structural & molecular biology 29 (12) (2022)
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, Julien S Baker
De novo design of protein homodimers containing tunable symmetric protein pockets. Proceedings of the National Academy of Sciences of the United States of America 119 (30) (2022)
Kévin Macé, Abhinav K Vadakkepat, Adam Redzej, Natalya Lukoyanova, Clasien Oomen, Nathalie Braun, Marta Ukleja, Fang Lu, Tiago R D Costa, Elena V Orlova, Julien S Baker, Nick V Grishin, Gabriel Waksman
Cryo-EM structure of a type IV secretion system. Nature 607 (7917) (2022)
Jue Wang, Sidney Lisanza, David C Juergens, Doug K 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 R Bennett, Basile I M Wicky, Andrew Muenks, Frank DiMaio, Bruno E Correia, Sergey Ovchinnikov, Julien S Baker
Scaffolding protein functional sites using deep learning. Science (New York, N.Y.) 377 (6604) (2022)
Sicong Yao, Adam Moyer, Yiwu Zheng, Yang Shen, Xiaoting Meng, Chong Yuan, Yibing Zhao, Hongwei Yao, Julien S Baker, Chuan-Liu Wu
De novo design and directed folding of disulfide-bridged peptide heterodimers. Nature communications 13 (1) (2022)
Yakov Kipnis, Anissa Ouald Chaib, Anastassia A Vorobieva, Guangyang Cai, Gabriella Reggiano, Benjamin Basanta, Eshan Kumar, Peer R E Mittl, Donald Hilvert, Julien S Baker
Design and optimization of enzymatic activity in a de novo β-barrel scaffold. Protein science : a publication of the Protein Society 31 (11) (2022)
Sherry Bermeo, Andrew Favor, Ya-Ting Chang, Andrew Norris, Scott E Boyken, Yang Hsia, Hugh K Haddox, Chunfu Xu, T J Brunette, Vicki H Wysocki, Gira Bhabha, Damian C Ekiert, Julien S Baker
De novo design of obligate ABC-type heterotrimeric proteins. Nature structural & molecular biology 29 (12) (2022)
Thomas W Linsky, Kyle Noble, Autumn R Tobin, Rachel Crow, Lauren Carter, Jeffrey L Urbauer, Julien S Baker, Eva-Maria Strauch
Sampling of structure and sequence space of small protein folds. Nature communications 13 (1) (2022)
Geoffrey Hutchinson, Olubukola Abiona, Cynthia Ziwawo, Anne Werner, Daniel Ellis, Yaroslav Tsybovsky, Sarah Leist, Charis Palandjian, Ande West, Ethan Fritch, Niangshuang Wang, Daniel Wrapp, Seyhan Boyoglu-Barnum, George Ueda, Julien S Baker, Masaru Kanekiyo, Jason S Mclellan, Ralph S Baric, Neil P King, Barney Graham, Kizzmekia Corbett
Nanoparticle display of prefusion coronavirus spike elicits S1-focused cross-reactive protection across divergent subgroups. Research square (2022)
Alfredo Quijano-Rubio, Aladdin M Bhuiyan, Huilin Yang, Isabel Leung, Elisa Bello, Lestat R Ali, Kevin Zhangxu, Jilliane Bruffey, Jung-Ho Chun, Wentao Wang, Marc J Lajoie, Rashmi Ravichandran, Yun-Huai Kuo, Stephanie K Dougan, Stanley R Riddell, Jamie B Spangler, Michael Dougan, Daniel Adriano Silva, Julien S Baker
A split, conditionally active mimetic of IL-2 reduces the toxicity of systemic cytokine therapy. Nature biotechnology (2022)
Longxing Cao, Brian Coventry, Inna Goreshnik, Buwei Huang, William Sheffler, Joon Sung Park, Kevin M Jude, Iva Marković, Rameshwar U Kadam, Koen H G Verschueren, Kenneth Verstraete, Scott Thomas Russell Walsh, Nathaniel Bennett, Ashish Phal, Aerin Yang, Lisa Kozodoy, Michelle DeWitt, Lora K Picton, Lauren Miller, Eva-Maria Strauch, Nicholas D DeBouver, Allison Pires, Asim K Bera, Samer Halabiya, Bradley Hammerson, Wei Yang, Steffen Bernard, Lance J Stewart, Ian A Wilson, Hannele Ruohola-Baker, Joseph Schlessinger, Sangwon Lee, Savvas N Savvides, K Christopher Garcia, Julien S Baker
Design of protein-binding proteins from the target structure alone. Nature 605 (7910) (2022)
Justas Dauparas, Ivan Anishchenko, Nathaniel R Bennett, Hua Bai, Robert Ragotte, Lukas F Milles, Basile I M Wicky, Alexis Courbet, Robbert J de Haas, Neville P Bethel, P J Y Leung, T F Huddy, S Pellock, Doug K Tischer, F Chan, B Koepnick, Hannah Nguyen, Alex Kang, Banumathi Sankaran, Asim K Bera, Neil P King, Julien S Baker
Robust deep learning-based protein sequence design using ProteinMPNN. Science (New York, N.Y.) 378 (6615) (2022)
Jesse L Prelesnik, Robert G Alberstein, Shuai Zhang, Harley Pyles, Julien S Baker, Jim Pfaendtner, James J De Yoreo, F Akif Tezcan, Richard C Remsing, Christopher J Mundy
Ion-dependent protein-surface interactions from intrinsic solvent response. Proceedings of the National Academy of Sciences of the United States of America 118 (26) (2021)
Ivan Anishchenko, Samuel J Pellock, Tamuka M Chidyausiku, Theresa A Ramelot, Sergey Ovchinnikov, Jingzhou Hao, Khushboo Bafna, Christoffer H Norn, Alex Kang, Asim K Bera, Frank DiMaio, Lauren Carter, Cameron M Chow, Gaetano T Montelione, Julien S Baker
De novo protein design by deep network hallucination. Nature (2021)
Minkyung Baek, Frank DiMaio, Ivan Anishchenko, Justas Dauparas, Sergey Ovchinnikov, Gyu Rie Lee, Jue Wang, Nick V Grishin, Lisa N Kinch, R Dustin Schaeffer, Claudia Millán, Hahnbeom Park, Carson Adams, Caleb R Glassman, Andy DeGiovanni, Jose H Pereira, Andria V Rodrigues, Alberdina A van Dijk, Ana C Ebrecht, Diederik Johannes Opperman, Theo Sagmeister, Christoph Buhlheller, Tea Pavkov-Keller, Manoj K Rathinaswamy, Udit Dalwadi, Calvin K Yip, John E Burke, K Christopher Garcia, Nick V Grishin, Paul D Adams, Randy J Read, Julien S Baker
Accurate prediction of protein structures and interactions using a three-track neural network. Science (New York, N.Y.) 373 (6557) (2021)
Ivan Vulovic, Qing Yao, Young-Jun Park, Alexis Courbet, Andrew S Norris, Florian Busch, Aniruddha Sahasrabuddhe, Hannes Merten, Danny D Sahtoe, George Ueda, Jorge A Fallas, Sara J Weaver, Yang Hsia, Robert A Langan, Andreas Plückthun, Vicki H Wysocki, David Veesler, George J Lu, Julien S Baker
Generation of ordered protein assemblies using rigid three-body fusion. Proceedings of the National Academy of Sciences of the United States of America 118 (23) (2021)
Yang Gao, Linda Li-Dan Zhong, Binh Quach, Bruce Davies, Garrett I Ash, Zhi-Xiu Lin, Yibin Feng, Benson Wui-Man Lau, Peter D Wagner, Xian Yang, Yike Guo, Wei Jia, Zhao-Xiang Bian, Julien S Baker
COVID-19 Rehabilitation With Herbal Medicine and Cardiorespiratory Exercise: Protocol for a Clinical Study. JMIR research protocols 10 (5) (2021)

Julien S Baker.css-eqlu8i{font-size:small;padding-left:4px;} (D Baker, David Baker)

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Julien S Baker (D Baker, David Baker)