Education
Sep 2019 - Aug 2026
Ph.D. in Physics (Integrated M.S./Ph.D. Program)
Sungkyunkwan University — Department of Physics
Specialization: Biological Physics / Bioinformatics
Expected degree conferral: August 25, 2026
GPA: 4.11 / 4.5 (96.1 / 100)
Advisor: Jejoong Yoo
Thesis: An in silico approach of protein folding and structure prediction
Mar 2016 - Aug 2019
Bachelor of Science in Physics
Sungkyunkwan University — Department of Physics, College of Sciences
GPA: 3.66 / 4.5 (91.6 / 100)
Research Interests
My research lies at the intersection of deep learning, protein structure prediction, and biomolecular simulation. Methodologically, I work with protein language models and optimal transport to compare and align proteins at evolutionary scale, and use molecular dynamics simulation and parallel/GPU computing to study and accelerate biomolecular systems.
Academic Positions
Korea Institute for Advanced Study
Research Assistant
2022 - Current
Honors and Awards
Apr 2025
Outstanding Presentation Award
2025 Korean Physical Society (KPS) Spring Meeting
DeepFold-PLM: Accelerating Protein Structure Prediction with Optimized Homolog Detection and Protein Language Models
Dec 2024
2nd Place, Antibody–Antigen Targets
16th Critical Assessment of Techniques for Protein Structure Prediction (CASP16)
Dec 2022
4th Place, Regular Targets
15th Critical Assessment of Techniques for Protein Structure Prediction (CASP15)
Publications
Software
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DeepFold-PLM — Accelerated protein structure prediction via efficient homology search using protein language models.
github.com/DeepFoldProtein/DeepFold-PLM
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OTalign — Optimal transport alignment for remote protein homologs using protein language model embeddings.
github.com/DeepFoldProtein/OTalign
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plmMSA — Unified MSA construction pipeline integrating the homology search of DeepFold-PLM and the optimal-transport alignment of OTalign.
github.com/DeepFoldProtein/plmMSA
Conference Presentations
Teaching
Teaching Assistant, Department of Physics, Sungkyunkwan University.
Spring 2023
Quantum Field Theory I (PHY5007) — O-Kab Kwon
Computational Physics (PHY2025) — Jejoong Yoo
Spring 2022
Biophysics (PHY3033) — Jejoong Yoo
Fall 2021
Biophysics (PHY5170) — Jejoong Yoo
Spring 2021
Biophysics (PHY3033) — Jejoong Yoo
Fall 2020
Electromagnetism I (PHY2010) — Dae-Joon Kang
Electromagnetism I, Problem Session (PHY2011) — Dae-Joon Kang
Spring 2020
Classical Mechanics I (PHY2001) — Jung Hoon Han
Classical Mechanics I, Problem Session (PHY2002) — Jung Hoon Han
Workshops and Schools Attended
Dec 2022
The 20th KIAS Protein Folding Winter School
Skills
Programming: C, C++, Python, Rust
ML Frameworks: PyTorch, JAX
Parallel/HPC: MPI, NCCL, CUDA, OpenAI Triton, SLURM
Containers: Docker, Apptainer
Molecular Dynamics: GROMACS, OpenMM
Bioinformatics: HMMER, MMseqs2, HH-suite