Publications

Recent publications (2023~2025)

Computational design of sequence-specific DNA-binding proteins

Cameron J Glasscock, Robert J Pecoraro, Ryan McHugh, Lindsey A Doyle, Wei Chen, Olivier Boivin, Beau Lonnquist, Emily Na, Yuliya Politanska, Hugh K Haddox, David Cox, Christoffer Norn, Brian Coventry, Inna Goreshnik, Dionne Vafeados, Gyu Rie Lee, Raluca Gordan, Barry L Stoddard, Frank DiMaio, David Baker

Nature Structural & Molecular Biology

Design of Orthogonal Far-Red, Orange and Green Fluorophore-binding Proteins for Multiplex Imaging

Long Tran, Shajesh Sharma, Steffen Klein, David Juergens, Justin Decarreau, Bingxu Liu, Yujia Wang, Asim K Bera, Alex Kang, Jon Woods, Emily Joyce, Dionne K Vafeados, Nicole Roullier, Wei Chen, Gyu Rie Lee, Julia Mahamid, Luke D Lavis, Linna An, David Baker

bioRxiv, 2025.08. 03.668343

De Novo Design of High-Performance Cortisol Luminescent Biosensors

Julie Yi-Hsuan Chen, Xue Peng, Chenggang Xi, Gyu Rie Lee, David Baker, Andy Hsien-Wei Yeh

Journal of the American Chemical Society 147 (31), 27494-27505

Atomic context-conditioned protein sequence design using LigandMPNN

Justas Dauparas, Gyu Rie Lee, Robert Pecoraro, Linna An, Ivan Anishchenko, Cameron Glasscock, David Baker

Nature Methods

De novo design of phospho-tyrosine peptide binders

Magnus S Bauer*, Jason Z Zhang*, Kejia Wu*, Gyu Rie Lee*, Brian Coventry*, Kody A Klupt, Jiuhan Shi, Rafael I Brent, Xinting Li, Carolina Moller, Nicole Roullier, Dionne K Vafeados, Indrek Kalvet, Rebecca K Skotheim, Siyu Zhu, Amir Motmaen, Luca C Herrmann, Pascal Sturmfels, Doug Tischer, Han Raut Altae-Tran, David Juergens, Rohith Krishna, Woody Ahern, Jason Yim, Asim K Bera, Alex Kang, Emily Joyce, Andrew Lu, Lance Stewart, Frank DiMaio, David Baker

bioRxiv, 2025.09. 29.678898

Modeling protein-small molecule conformational ensembles with chemnet

Ivan Anishchenko, Yakov Kipnis, Indrek Kalvet, Guangfeng Zhou, Rohith Krishna, Samuel J Pellock, Anna Lauko, Gyu Rie Lee, Linna An, Justas Dauparas, Frank DiMaio, David Baker

bioRxiv

Binding and sensing diverse small molecules using shape-complementary pseudocycles

Linna An, Meerit Said*, Long Tran*, Sagardip Majumder,* Inna Goreshnik, Gyu Rie Lee, David Juergens, Justas Dauparas, Ivan Anishchenko, Brian Coventry, Asim K Bera, Alex Kang, Paul M Levine, Valentina Alvarez, Arvind Pillai, Christoffer Norn, David Feldman, Dmitri Zorine, Derrick R Hicks, Xinting Li, Mariana Garcia Sanchez, Dionne K Vafeados, Patrick J Salveson, Anastassia A Vorobieva, David Baker

Science 385 (6706), 276-282

Protein ensemble generation through variational autoencoder latent space sampling

Sanaa Mansoor, Minkyung Baek, Hahnbeom Park, Gyu Rie Lee, David Baker

Journal of Chemical Theory and Computation 20 (7), 2689-2695

Generalized biomolecular modeling and design with RoseTTAFold All-Atom

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 Vafeados, Xinting Li, George A Sutherland, Andrew Hitchcock, C Neil Hunter, Alex Kang, Evans Brackenbrough, Asim K Bera, Minkyung Baek, Frank DiMaio, David Baker

Science 384 (6693), eadl2528

De novo design of high-affinity binders of bioactive helical peptides

Susana Vázquez Torres, Philip JY Leung, Preetham Venkatesh, Isaac D Lutz, Fabian Hink, Huu-Hien Huynh, Jessica Becker, Andy Hsien-Wei Yeh, David Juergens, Nathaniel R Bennett, Andrew N Hoofnagle, Eric Huang, Michael J MacCoss, Marc Expòsit, Gyu Rie Lee, Asim K Bera, Alex Kang, Joshmyn De La Cruz, Paul M Levine, Xinting Li, Mila Lamb, Stacey R Gerben, Analisa Murray, Piper Heine, Elif Nihal Korkmaz, Jeff Nivala, Lance Stewart, Joseph L Watson, Joseph M Rogers, David Baker

Nature 626 (7998), 435-442

Small-molecule binding and sensing with a designed protein family

Gyu Rie Lee*, Samuel J Pellock*, Christoffer Norn*, Doug Tischer, Justas Dauparas, Ivan Anischenko, Jaron AM Mercer, Alex Kang, Asim Bera, Hannah Nguyen, Inna Goreshnik, Dionne Vafeados, Nicole Roullier, Hannah L Han, Brian Coventry, Hugh K Haddox, David R Liu, Andy Hsien-Wei Yeh, David Baker

bioRxiv, 2023.11. 01.565201

De novo design of luciferases using deep learning

Andy Hsien-Wei Yeh*, Christoffer Norn*, Yakov Kipnis, Doug 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, KN Houk, David Baker

Nature 614 (7949), 774-780

Evaluating GPCR modeling and docking strategies in the era of deep learning-based protein structure prediction

Sumin Lee*, Seeun Kim*, Gyu Rie Lee*, Sohee Kwon, Hyeonuk Woo, Chaok Seok, Hahnbeom Park

Computational and Structural Biotechnology Journal 21, 158-167