Minkyung Baek (M Baek)

Publication Activity (10 Years)

Years Active: 2021-2024
Publications (10 Years): 39

Top Topics

Protein Protein

Acinetobacter Baumannii

Top Venues

Science (New York, N.Y.)

Nature communications

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

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

Publications

Meghana Kshirsagar, Artur Meller, Ian Humphreys, Samuel Sledzieski, Yixi Xu, Rahul Dodhia, Eric Horvitz, Bonnie Berger, Gregory R Bowman, Juan Lavista Ferres, Julien S Baker, Minkyung Baek
Rapid and accurate prediction of protein homo-oligomer symmetry with Seq2Symm. Research square (2024)
Rohith Krishna, Jue Wang, Woody Ahern, Pascal Sturmfels, Preetham Venkatesh, Indrek Kalvet, Gyu Rie Lee, Felix S Morey-Burrows, Ivan Anishchenko, Ian R Humphreys, Ryan McHugh, Dionne K Vafeados, Xinting Li, George A Sutherland, Andrew Hitchcock, Christopher Neil Hunter, Alex Kang, Evans Brackenbrough, Asim K Bera, Minkyung Baek, Frank Dimaio, Julien S Baker
Generalized biomolecular modeling and design with RoseTTAFold All-Atom. Science (New York, N.Y.) 384 (6693) (2024)
Ian R Humphreys, Jing Zhang, Minkyung Baek, Yaxi Wang, Aditya Krishnakumar, Jimin Pei, Ivan Anishchenko, Catherine A Tower, Blake A Jackson, Thulasi Warrier, Deborah T Hung, S Brook Peterson, Joseph D Mougous, Qian Cong, Julien S Baker
Protein interactions in human pathogens revealed through deep learning. Nature microbiology (2024)
Minkyung Baek
Towards the prediction of general biomolecular interactions with AI. Nature methods 21 (8) (2024)
Rohith Krishna, Jue Wang, Woody Ahern, Pascal Sturmfels, Preetham Venkatesh, Indrek Kalvet, Gyu Rie Lee, Felix S Morey-Burrows, Ivan Anishchenko, Ian R Humphreys, Ryan McHugh, Dionne K Vafeados, Xinting Li, George A Sutherland, Andrew Hitchcock, Christopher Neil Hunter, Alex Kang, Evans Brackenbrough, Asim K Bera, Minkyung Baek, Frank Dimaio, Julien S Baker
Generalized biomolecular modeling and design with RoseTTAFold All-Atom. Science (New York, N.Y.) (2024)
Meghana Kshirsagar, Artur Meller, Ian Humphreys, Samuel Sledzieski, Yixi Xu, Rahul Dodhia, Eric Horvitz, Bonnie Berger, Gregory R Bowman, Juan Lavista Ferres, Julien S Baker, Minkyung Baek
Rapid and accurate prediction of protein homo-oligomer symmetry with Seq2Symm. Research square (2024)
Rohith Krishna, Jue Wang, Woody Ahern, Pascal Sturmfels, Preetham Venkatesh, Indrek Kalvet, Gyu Rie Lee, Felix S Morey-Burrows, Ivan Anishchenko, Ian R Humphreys, Ryan McHugh, Dionne K Vafeados, Xinting Li, George A Sutherland, Andrew Hitchcock, Christopher Neil Hunter, Alex Kang, Evans Brackenbrough, Asim K Bera, Minkyung Baek, Frank Dimaio, Julien S Baker
Generalized biomolecular modeling and design with RoseTTAFold All-Atom. Science (New York, N.Y.) 384 (6693) (2024)
Minkyung Baek
Towards the prediction of general biomolecular interactions with AI. Nature methods 21 (8) (2024)
Rohith Krishna, Jue Wang, Woody Ahern, Pascal Sturmfels, Preetham Venkatesh, Indrek Kalvet, Gyu Rie Lee, Felix S Morey-Burrows, Ivan Anishchenko, Ian R Humphreys, Ryan McHugh, Dionne K Vafeados, Xinting Li, George A Sutherland, Andrew Hitchcock, Christopher Neil Hunter, Alex Kang, Evans Brackenbrough, Asim K Bera, Minkyung Baek, Frank Dimaio, Julien S Baker
Generalized biomolecular modeling and design with RoseTTAFold All-Atom. Science (New York, N.Y.) 384 (6693) (2024)
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)
Samuel Sledzieski, Meghana Kshirsagar, Minkyung Baek, Bonnie Berger, Rahul Dodhia, Juan M Lavista Ferres
Democratizing Protein Language Models with Parameter-Efficient Fine-Tuning. bioRxiv : the preprint server for biology (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)
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)
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)
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)
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)
Nathaniel R Bennett, Brian Coventry, Inna Goreshnik, Buwei Huang, Aza Allen, Dionne K 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)
Minkyung Baek, Ryan McHugh, David Baker, 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)
Nathaniel R Bennett, Brian Coventry, Inna Goreshnik, Buwei Huang, Aza Allen, Dionne K 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)
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)
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)
Nathaniel R Bennett, Brian Coventry, Inna Goreshnik, Buwei Huang, Aza Allen, Dionne K 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)
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)
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)
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)
Nathaniel R Bennett, Brian Coventry, Inna Goreshnik, Buwei Huang, Aza Allen, Dionne K 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)
Basile I M Wicky, Lukas F Milles, Alexis Courbet, Robert J 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)
Jue Wang, Sidney Lisanza, David C Juergens, Doug K Tischer, Joseph L Watson, Karla M Castro, Robert J Ragotte, Amijai Saragovi, Lukas F Milles, Minkyung Baek, David Baker, 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)
Manoj K Rathinaswamy, Udit Dalwadi, Kaelin D Fleming, Carson Adams, Jordan T B Stariha, Els Pardon, Minkyung Baek, Oscar Vadas, Frank Dimaio, Jan Steyaert, Scott D Hansen, Calvin K Yip, John E Burke
Structure of the phosphoinositide 3-kinase (PI3K) p110γ-p101 complex reveals molecular mechanism of GPCR activation. Science advances 7 (35) (2021)
Minkyung Baek, Frank Dimaio, David Baker, 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 Henrique 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)
David Baker, Minkyung Baek, Hahnbeom Park, Naozumi Hiranuma, David E Kim, Justas Dauparas, Sanaa Mansoor, Ian R Humphreys, David Baker
Protein tertiary structure prediction and refinement using deep learning and Rosetta in CASP14. Proteins 89 (12) (2021)
Ian R Humphreys, Jimin Pei, Minkyung Baek, Aditya Krishnakumar, David Baker, Sergey Ovchinnikov, Jing Zhang, Travis J Ness, Sudeep Banjade, Saket Rahul 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, Nick V Grishin, Julien S Baker
Computed structures of core eukaryotic protein complexes. Science (New York, N.Y.) 374 (6573) (2021)
Minkyung Baek, Ivan Anishchenko, Hahnbeom Park, Ian R Humphreys, David Baker
Protein oligomer modeling guided by predicted interchain contacts in CASP14. Proteins 89 (12) (2021)
Naozumi Hiranuma, Hahnbeom Park, Minkyung Baek, David Baker, Justas Dauparas, Julien S Baker
Improved protein structure refinement guided by deep learning based accuracy estimation. Nature communications 12 (1) (2021)