zsasa: a Zig-based engine for high-throughput solvent accessible surface area at proteome scale
Tsubasa Nagae, Kentaro Tomii — bioRxiv, 2026
Publications
Papers
2026
Talks & Posters
2026
Building an AI drug discovery information platform through comprehensive data collection and analysis of middle molecule-target interaction
Kazuyoshi Ikeda, Tsubasa Nagae, Yugo Shimizu, Kentaro Tomii — The 146th Annual Meeting of the Pharmaceutical Society of Japan, 2026
zsasa: a high-performance SASA calculator implemented in Zig
Tsubasa Nagae, Kentaro Tomii — The 26th Annual Meeting of the Protein Science Society of Japan, 2026
2025
Building a protein-ligand interaction database for mid-molecular drug discovery research: a comprehensive analysis of the Protein Data Bank.
Tsubasa Nagae, Kazuyoshi Ikeda, Kentaro Tomii — The 145th Annual Meeting of the Pharmaceutical Society of Japan, 2025
Development of an Integrated Machine Learning Model for the Design and Prediction of PPI Modulators
Tsubasa Nagae, Kohei Soda, Kazuyoshi Ikeda, Masashi Tsubaki, Kentaro Tomii — Chem-Bio Informatics Society Annual Meeting 2025, 2025
2024
Building a Comprehensive Dataset for the Rational Design of Molecular Glue Degraders
Tsubasa Nagae, Kohei Soda, Kazuyoshi Ikeda, Masashi Tsubaki, Kentaro Tomii — The 144th Annual Meeting of the Pharmaceutical Society of Japan, 2024
AI 駆動型データキュレーションによる持続可能な中分子相互作用統合データベースの開発
Kazuyoshi Ikeda, Tsubasa Nagae, Tomoki Yonezawa, Kentaro Tomii — Togo Day Symposium 2024, 2024
AI駆動型データキュレーションによる中分子相互作用統合データベースの開発
Kazuyoshi Ikeda, Tsubasa Nagae, Tomoki Yonezawa, Kentaro Tomii — Togo Day Symposium 2024, 2024
AlphaFold3 のリガンドはどこからやってくる？
Tsubasa Nagae, Kentaro Tomii — The 16th Annual Meeting of the Young Researchers' Association for Computational and Omics Biology, 2024
Construction of PPI Stabilizers and Inhibitors Dataset for Rational Design of Molecular Glue Degraders
Tsubasa Nagae, Kohei Soda, Kazuyoshi Ikeda, Masashi Tsubaki, Kentaro Tomii — The 24th Annual Meeting of the Protein Science Society of Japan, 2024
Development of an Integrated Machine Learning Model Incorporating Compound-Protein Information for Design and Prediction of Small-Molecule Modulators of PPIs
Tsubasa Nagae, Kohei Soda, Kazuyoshi Ikeda, Masashi Tsubaki, Kentaro Tomii — Chem-Bio Informatics Society Annual Meeting 2024, 2024
Other
2026
OpenADMET PXR Blind Challenge Activity Track — 4th place
N283T — OpenADMET PXR Blind Challenge, 2026
2024
深層学習ベースのドッキング手法の限界と課題 — PoseBusters による化学的・物理的妥当性の評価
Tsubasa Nagae — CBI学会誌, 2024