Seoul National University Biological Sciences Website

논문

Laboratory of Computational Structural and Systems Biology

Alzheimer's Research & Therapy

Han-Byul Kim, Sangjin Yoo, Hoyun Kwak, Shi-Xun Ma, Ryunhee Kim, Minhyeok Lee, Nui Ha, Soonil Pyo, Soon-Gu Kwon, Eun-Ho Cho, Sang-Myeong Lee, Juwon Jang, Won Kyum Kim, Hae-Chul Park, Minkyung Baek, Yosub Park, Ji-Young Park, Jin-Woo Park, Sun Wook Hwang, Jong-Ik Hwang, Jae Young Seong (2025). Inhibition of FAM19A5 reverses synaptic loss and cognitive decline in mouse models of Alzheimer’s disease. Alzheimer's Research & Therapy, 17(1), 168.

Current Opinion in Structural Biology

Sanggeun Park#, Sojung Myung#, Minkyung Baek* (2025). Advancing protein structure prediction beyond AlphaFold2. Current Opinion in Structural Biology, 90(), 102985.

#co-first authors

Min Su Yoon#, Byunghyun Bae#, Kunhee Kim#, Hahnbeom Park*, Minkyung Baek* (2025). Deep learning methods for proteome-scale interaction prediction. Current Opinion in Structural Biology, 90(), 102981.

#co-first authors, *co-corresponding authors

Journal of Biological Chemistry

Mark R MacRae, Dhenesh Puvanendran, Max AB Haase, Nicolas Coudray, Ljuvica Kolich, Cherry Lam, Minkyung Baek, Gira Bhabha, Damian C Ekiert (2023). Protein-protein interactions in the Mla lipid transport system probed by computational structure prediction and deep mutational scanning. Journal of Biological Chemistry, 299(6), 104744.

Nature

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 IM 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, David Baker (2023). De novo design of protein structure and function with RFdiffusion. Nature, 620(7976), 1089–1100.

Nature Communications

Meghana Kshirsagar*, Artur Meller, Ian R. Humphreys, Samuel Sledzieski, Yixi Xu, Rahul Dodhia, Eric Horvitz, Bonnie Berger, Gregory R. Bowman, Juan Lavista Ferres, David Baker, Minkyung Baek* (2025). Rapid and accurate prediction of protein homo-oligomer symmetry using Seq2Symm. Nature Communications, (), .

*Co-corresponding authors

Nathaniel R Bennett, Brian Coventry, Inna Goreshnik, Buwei Huang, Aza Allen, Dionne Vafeados, Ying Po Peng, Justas Dauparas, Minkyung Baek, Lance Stewart, Frank DiMaio, Steven De Munck, Savvas N Savvides, David Baker (2023). Improving de novo protein binder design with deep learning. Nature Communications, 14(1), 2625.

Eliza S Nieweglowska, Axel F Brilot, Melissa Méndez-Moran, Claire Kokontis, Minkyung Baek, Junrui Li, Yifan Cheng, David Baker, Joseph Bondy-Denomy, David A Agard (2023). The ϕPA3 phage nucleus is enclosed by a self-assembling 2D crystalline lattice. Nature Communications, 14(1), 927.

Nature Methods

Minkyung Baek, Ryan McHugh, Ivan Anishchenko, Hanlun Jiang, David Baker, Frank DiMaio (2024). Accurate prediction of protein–nucleic acid complexes using RoseTTAFoldNA. Nature Methods, 21(1), 117-121.

Nature Microbiology

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*, David Baker* (2024). Protein interactions in human pathogens revealed through deep learning. Nature Microbiology, 9(), 2642–2652.

#co-first authors, *co-corresponding authors

Proceedings of the National Academy of Sciences

Amir Motmaen, Justas Dauparas, Minkyung Baek, Mohamad H Abedi, David Baker, Philip Bradley (2023). Peptide-binding specificity prediction using fine-tuned protein structure prediction networks. Proceedings of the National Academy of Sciences, 120(9), e2216697120.

Proteins: Structure, Function, and Bioinformatics

Minkyung Baek, Ivan Anishchenko, Hahnbeom Park, Ian R Humphreys, David Baker (2021). Protein oligomer modeling guided by predicted interchain contacts in CASP14. Proteins: Structure, Function, and Bioinformatics, 89(12), 1824-1833.

Ivan Anishchenko#, Minkyung Baek#, Hahnbeom Park#, Naozumi Hiranuma, David E Kim, Justas Dauparas, Sanaa Mansoor, Ian R Humphreys, David Baker (2021). Protein tertiary structure prediction and refinement using deep learning and Rosetta in CASP14. Proteins: Structure, Function, and Bioinformatics, 89(12), 1722-1733.

# co-first authors

Science

Jing Zhang, Ian R Humphreys, Jimin Pei, Jinuk Kim, Chulwon Choi, Rongqing Yuan, Jesse Durham, Siqi Liu, Hee-Jung Choi, Minkyung Baek, David Baker, Qian Cong (2025). Predicting protein-protein interactions in the human proteome. Science, 390(6771), eadt1630.

Isaac D Lutz, Shunzhi Wang, Christoffer Norn, Alexis Courbet, Andrew J Borst, Yan Ting Zhao, Annie 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, David Baker (2023). Top-down design of protein architectures with reinforcement learning. Science, 380(6642), 266-273.

BIM Wicky, LF Milles, A Courbet, RJ Ragotte, J Dauparas, E Kinfu, S Tipps, RD Kibler, M Baek, F DiMaio, X Li, L Carter, A Kang, H Nguyen, AK Bera, D Baker (2022). Hallucinating symmetric protein assemblies. Science, 378(6615), 56-61.

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 IM Wicky, Andrew Muenks, Frank DiMaio, Bruno Correia, Sergey Ovchinnikov, David Baker (2022). Scaffolding protein functional sites using deep learning. Science, 377(6604), 387-394.

Ian R Humphreys# Jimin Pei#, Minkyung Baek#, Aditya Krishnakumar#, et al. (2021). Computed structures of core eukaryotic protein complexes. Science, 374(6573), eabm4805.

# co-first authors

Minkyung Baek, et al. (2021). Accurate prediction of protein structures and interactions using a three-track neural network. Science, 373(6557), 871-876.