+: equal contribution

Submitted/Preprint

• mechanoLight: a genetically encoded fluorescent biosensor for visualizing 5-HT2AR mechanotransduction in live cells.
  I-Y Baek+, H. Kim+, D. Kwon+, H. Park, J. Seong*.

• G-screen: Scalable Receptor-Aware Virtual Screening through Flexible Ligand Alignment.
  N. Jung, H. Park, J. Yang*, and C. Seok* (bioRxiv: Link).

• PrOMet: Accurate and Robust Metal-binding site and Type Prediction.
  G. Park, C. Seok*, H. Park*

• S100A4 Promotes Collective Invasion of Pancreatic Ductal Adenocarcinoma and Its Blockade Suppresses Metastasis.
  D. Son, Y. Lim, C. W. Yu, M. J. Cha, E. Lee, H. Kim, H. Lee, H Park, S. M. Hong, S. Chang*.

• Revealing ligand-specific activation of 5-HT7R through functional roles of key residues in Gs signaling and biased agonism.
  E. Park+, H. Lee+, T. Kang, K. Lim, S. Lee, H. Choo*, A. Lee*, H. Park*, B. Jeon*. 

• Transcriptional stalling by p16INK4a impairs mitochondrial bioenergetics and cognitive function in Alzheimer’s disease.
  S.J. Hyeon+, P.T.T. Nguyen+, C. Park+, Y-E Han+, U. Park, H.S. Moon, E.H. Lee, J. Chu, S. Kim, S.H. Choi, H. Lee, T.D. Stein, H. Park, S-J Oh*, J. Lee*, H. Ryu*

2026

• MotifLeadDB: A Hierarchical Structural Dataset for Congeneric Ligand Binding Free Energy Change
  N. Kim, B. Bae, N. Jung, C. Seok, H. Park*, J Chem Info Model, accepted.

• ProMiSE: Protein Multi-state Structure Evaluation Benchmark in Biological Contexts.
  B. Ku+, S. Kim+, Y. Kim+, H. Park*, C. Seok*, ICML, accepted.

• Using experimental results of protein design to guide biomolecular energy-function development.
  H.K. Haddox*, G.J. Rocklin, F.C. Motta, D. Strickland, S.F. Halabiya, C. Cordray, H. Park, E. Klavins, D. Baker, F. DiMaio*, PLOS Comput. Biol. 2026. Link 

• AI-guided engineering of FAD-glucose dehydrogenase for enhanced processibility and functional performance.
  S-J Lee+, S. Min+, Y-J Han, S-R Go, K-H Park, H Park*, E-J Woo*. Chem Eng J Adv, 2026. Link (+: equal contribution)

• Interpretable Machine Learning for Protein Science: Structure, Function, and Interactions.
  L. F. Vecchietti, M. Lee, B. Hangeldiyev, H. Jung, H. Park, T-K. Kim, M. Cha, H.M. Kim*, ACM Computing surveys, 2026. Link

• Protein folding stability estimation with explicit consideration of unfolded states.
  H. Lee, Y.G. Cho, J. Yoon, M. Steinegger, H.M. Kim*, H. Park*, Nat Commun., 2026. Link.

2025

• SHARP: Generating Synthesizable Molecules via Fragment-based Hierarchical Action-space Reinforcement Learning for Pareto Optimization.
  J. Kim, S. Ryu, H. Park*, C. Seok*, J Chem Info Modeling 65, 2025. Link

• Deep learning molecular interaction motifs from Receptor structure alone.
  S. Kim, S. Oh, H. Woo, J. Sim, C. Seok*, H. Park*, J Cheminfo 17, 2025. Link 

• Artificial intelligence-driven discovery of novel scaffolds for selective TLR7 antagonists and their application in enhancing mRNA translation efficiency.
  S. Yoo, K. Yoon, N. Kim, G. Keum, H. Park*, E-K. Bang*, Eur. J. Pharm. Sci., 2025. Link 

• Physics-inspired accuracy estimator for model-docked ligand complexes.
  B. Bae, J. Choi, C. Seok, H. Park*, J Chem Theory Comput 21, 2025. Link 

• Deep Learning Methods for Proteome-scale Interaction Prediction.
  M. S. Yoon+, B. Bae+, K. Kim+, H. Park*, M. Baek*, Curr Opinion Struct Biol. 90, 2025. Link (+: equal contribution)

2024

• An artificial intelligence accelerated virtual screening platform for drug discovery.
  G. Zhou, D-V Rusnac, H. Park, D. Canzani, H. M. Nguyen, L. Stewart, M. F. Bush, P. T. Nguyen, H. Wulff, V. Yarov-Yarovoy, N. Zheng*, Frank DiMaio*, Nat Commun. 15, 2024. Link 

• GalaxyDock-DL: Protein–Ligand Docking by Global Optimization and Neural Network Energy.
  C-S. Lee, J. Won, S. Ryu, J. Yang, N. Jung, H. Park, C. Seok, J Chem. Theory Comput. 20, 2024. Link 

• Protein Ensemble Generation through Variational Autoencoder Latent Space Sampling.
  S. Mansoor, M. Baek, H. Park, GR Lee, D. Baker*. J Chem. Theory Comput 20. 2024. Link

2022~2023

• Understanding the molecular mechanisms of odorant binding and activation of the human OR52 family.
  C. Choi+, J. Bae+, S. Kim, S. Lee, H. Kang, J. Kim, I. Bang, K. Kim, W-K Huh, C. Seok, H. Park, W. Im, H-J Choi*, Nat Commun 14, 2023. (+: equal contribution) Link 

•  Development of a novel histone deacetylase inhibitor unveils the role of HDAC11 in alleviating depression by inhibition of microglial activation.
  S. Y. Baek, J. Lee, T. Kim, H. Lee, H-S Choi, H. Park, M. Koh, E. Kim, M. E. Jung, D. Iliopoulos, J-Y Lee, J. Kim*, S. Lee*. Biomedicine & Pharmacotherapy 2023. Link 

• Benchmarking applicability of medium-resolution cryo-EM structures for structure-based drug design.
  S. Lee, C. Seok*, and H. Park*, J Comput Chem, 2023. Link 

• Evaluating GPCR modeling and docking strategies in the era of deep learning-based protein structure prediction.
  S. Lee+, S. Kim+, GR Lee+, S. Kwon, H. Woo, C. Seok*, and H. Park*, Comput Struct Biotechnol J, 2022. (+: equal contribution) Link 

• Pseudo-Isolated α-Helix Platform for the Recognition of Deep and Narrow Targets.
  D. Kim, S. Han, H. Park, S. Choi, M. Kaur, E. Hwang, S. Han, J. Ryu, H-K Cheong, R. P. Barnwal*, and Y. Lim*. JACS 2022. Link 

Pre-KIST selected papers (~2021):

Full list can be found in google scholar: https://scholar.google.com/citations?user=Y8Tqu4MAAAAJ&hl=ko

DeepAccNet paper:

• N. Hiranuma1, H. Park1 (co-first), M. Baek, I. Anishchanka, J. Dauparas, D. Baker. Improved protein structure refinement guided by deep learning based accuracy estimation, Nat Commun 12, 1340. https://doi.org/10.1038/s41467-021-21511-x, 2021.

RosettaGenpot & GALigandDock paper:

• H. Park, G. Zhou, M. Baek, D. Baker, F. DiMaio. Force Field Optimization Guided by Small Molecule Crystal Lattice Data Enables Consistent Sub-Angstrom Protein–Ligand Docking. J Chem Theory Comput., 2021.

Refinement method for the CASP13 (2018) refinement category winner:

• H. Park, S. Ovchinnikov, D. E. Kim, F. DiMaio, D. Baker, Protein homology model refinement by large scale energy optimization, Proc Natl Acad Sci USA 115, 3054-3059, 2018.

First large-scale study showing how sequence co-evolution can inform the protein structure: 

• S. Ovchinnikov, H. Park, N. Varghese, P. Huang, G. A. Pavlopoulos, D. E. Kim, H. Kamisetty, N. C. Kyrpides, and D. Baker, Protein structure determination using metagenome sequence data, Science 355, 294-298, 2017.

Rosetta standard energy function "REF2015" original paper:

• H. Park, P. Bradley, P. Greisen Jr., Y. Liu, V. K. Mulligan, D. E. Kim, D. Baker, and F. DiMaio. Simultaneous optimization of biomolecular energy function on features from small molecules and macromolecules, J Chem Theory Comput. 12, 6201-6212, 2016.*