Structural biology · Protein design · Lysosomal disease mechanisms
구조생물학 · 단백질 설계 · 리소좀 질환 기전 · 화학공학적 공정 렌즈
I work at the intersection of structural reasoning and design-oriented problem framing for lysosomal enzymes. My current focus is iduronate-2-sulfatase (IDS) and mucopolysaccharidosis type II (Hunter syndrome): how missense variants disrupt interaction networks that support folding, ER quality control, and catalytic competence—not only active-site chemistry.
I care about questions that stay scientifically honest:
- What can be claimed from a crystal structure (PDB 5FQL) and public variant data—before wet-lab residual activity is in hand?
- When AlphaFold returns near-WT folds for pathogenic alleles, what does that not tell us about stability or trafficking?
- How should surface interfaces be chosen for stabilization strategies when the disease node is fully buried?
- How does a chemical-engineering lens (mass balance, unit operations, fault modes, gated scale-up) reframe “measured activity loss”?
목표는 “예쁜 결합”이 아니라 기능적 구조(competence)의 회복 가능성을 구조적으로 가늠하는 일입니다.
IDSX Lab — Structure-guided decision layer for IDS
| Live site | thilo-yoo.github.io/idsx-lab |
| Repository | thilo-yoo/idsx-lab |
| Master package (2026-07) | Portal page · Chronicle · 12-mo plan · Advisor deck (PPTX) |
| Target | Human IDS · UniProt P22304 · PDB 5FQL |
What it is
A public research portal documenting a structure-first triage of IDS missense variants for chaperone / stabilizer amenability as a proxy—with explicit non-claims (no therapeutic efficacy asserted).
2026-07 Master package adds
- Development chronicle (what was built, in order, without over-summarizing)
- Strength map (which layers are solid vs open)
- Track A (module + surface patch) vs Track B (neo-pocket / CTSS) tension, stated honestly
- 90-day and 12-month gated execution plan
- 30-slide advisor Keynote/PPTX for faculty / expert consultation
- Chemical-engineering symbolic frame (throughput of functional enzyme molecules)
Core ideas
- Disease hotspot ≠ binder interface: buried nodes (e.g. Ser152 module) vs adjacent surface patches
- Success metric: catalytic competence, not docking score alone
- ER quality control reads folding state, not primary-sequence “letters”
- Thermal stability is a readout, not the project title
- AlphaFold Server: WT / S152I / multi-hotspot cocktails → near-identical global folds; interpret with discipline
Stack / methods
Structure annotation · ClinVar/UniProt mapping · amenability rules · AF Server analysis · ΔΔG/CTSS exploration · static documentation site
AnjeonDong — Multisensory street safety (Dongjak)
| Repository | thilo-yoo/anjeondong-safety |
| Focus | Lenticular PETG fencing · multisensory construction-edge kit · map-layer safety awareness |
Policy-league work for Dongjak-gu redevelopment streets: angle-triggered warnings (distance / eye-height / slope), plus a AnjeonDong concept for data-informed detours on everyday map UX. Curated visuals retained for reuse.
- Lysosomal storage disorders (MPS II and related LSD logic)
- Pharmacological chaperones as condition libraries (e.g. GCase–ambroxol as reference, not off-target prescription)
- De novo binder design pipelines (RFdiffusion-class tools) as downstream of structural triage
- Process-engineering metaphors for trafficking / quality control
- Clear scientific writing: claim / non-claim hygiene
- IDSX portal: https://thilo-yoo.github.io/idsx-lab/
- Master package: https://thilo-yoo.github.io/idsx-lab/pages/master-package.html
- AF job catalog: https://thilo-yoo.github.io/idsx-lab/pages/af-catalog.html
- Framework note: https://thilo-yoo.github.io/idsx-lab/pages/framework.html
- Research chronicle (repo): https://github.com/thilo-yoo/idsx-lab/blob/main/docs/master-package/01_research_chronicle.md
- Gap checklist (what next): https://github.com/thilo-yoo/idsx-lab/blob/main/docs/master-package/06_gap_checklist.md
- Process KPI page: https://thilo-yoo.github.io/idsx-lab/pages/process-kpi.html
- ChemE framework: https://github.com/thilo-yoo/idsx-lab/blob/main/docs/master-package/04_chemeng_framework.md
Work shared here is an early, structure-driven research frame—useful for prioritization and dialogue with structural/design mentors—not a completed therapeutic program.
학부·예비 연구 단계의 구조 기반 질문 설정과 공개 기록소입니다. 치료 주장이 아닙니다.
