Seoul National University Biological Sciences Website

논문

Laboratory of Computational Structural and Systems Biology

2024

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.

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 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.

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.

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.

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.

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.

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.

2022

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.

2021

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

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.