Nagae TsubasaNagae Tsubasa

About

I work in bioinformatics and chemoinformatics, with a focus on structural bioinformatics — reading protein structures and their interactions through computation. Beyond machine learning and AI, I'm just as drawn to databases and data infrastructure. I also pour energy into building analysis tools and ChimeraX / VS Code extensions to make research faster and more fun.

Interests

• Structural bioinformatics
• Bioinformatics
• Chemoinformatics
• Machine learning & AI
• Databases
• Research tooling & extensions

Education

1. 2019–2023Functional Molecular Design Lab, Faculty of Agriculture, Shinshu University (B.S.)B.S. thesis: “Development of a Cryptic Binding Site Modeling Method from Apo Structures Using Normal Mode Analysis”
2. 2023–2025M.S. program, Graduate School of Medical Life Science, Yokohama City UniversityM.S. thesis: “Building a Foundation for the Informatics Analysis of Protein–Protein Interaction Modulators”
3. 2025–Ph.D. program, Graduate School of Medical Life Science, Yokohama City University (current)

Awards, grants & projects

1. 2025Selected for the Data-Thinking Innovative Human Resources Program (SPRING), FY2025Research theme: Development of AI for Integrated Understanding of Protein-Protein Interaction Modulators
2. 2024Development of a sustainable database for middle molecules using AI-driven data curationDatabase Integration Coordination Program (DICP), JPMJND2401 / since June 2024
3. 2024Outstanding Student Presentation Award (Poster)The 144th Annual Meeting of the Pharmaceutical Society of Japan (Yokohama)
4. 2023効率的な分解誘導薬創成に向けた分子設計AIの基盤開発NEDO先導研究プログラム（1228013）／2023年9月〜2024年3月

Academic societies

• Chem-Bio Informatics Society (CBI)
• The Pharmaceutical Society of Japan
• The Protein Science Society of Japan

I belong to these societies, but don't necessarily attend every annual meeting.

Contact

• w255508b [at] yokohama-cu.ac.jp

Replace [at] with @ to email me.