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2023 Fiscal Year Final Research Report

Development of PyDISH, the analytic tool of the structure-function relationship for heme

Research Project

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Project/Area Number 21K14741
Research Category

Grant-in-Aid for Early-Career Scientists

Allocation TypeMulti-year Fund
Review Section Basic Section 37010:Bio-related chemistry
Research InstitutionHiroshima University

Principal Investigator

Kanematsu Yusuke  広島大学, 先進理工系科学研究科(工), 助教 (10765936)

Project Period (FY) 2021-04-01 – 2024-03-31
Keywords統計科学 / 機械学習 / バイオインフォマティクス / 量子化学
Outline of Final Research Achievements

To improve the applicability of PyDISH, the application for structure-function relationship analysis of heme proteins, we implemented automatic database update and analytic interface of user-uploaded structures, respectively. We also validated the prediction of functional classification using the random forest method, and confirmed that it is possible to perform binary classification of functions with significant accuracy based on structural distortion of heme porphyrin. We also implemented a tool to evaluate approximate values of redox potential and oxygen adsorption capacity based on the given heme structure. Meanwhile, by diverting the algorithm of PyDISH's automatic update, we implemented and published another application to perform statistical analysis on arbitrary metal cofactors using Google Colab, and confirmed its usefulness.

Free Research Field

生物物理化学

Academic Significance and Societal Importance of the Research Achievements

本研究におけるPyDISHの開発とGoogle Colabを用いた新規解析機能により、誰でもWebブラウザ上で最新のデータを参照しながら特定のヘムや金属補因子の特徴づけを行うことが新たに可能になった。これにより実験やシミュレーションで取得されたヘムの構造歪みに対する意味づけが可能になった。また、タンパク質に結合したヘムの構造を予測する機能を新規実装した構造予測ツール「AlphaFold3」とPyDISHとの併用により、新規タンパク質の活性を予測することも可能になった。ただしその予測精度や適用範囲については今後系統的に検討する必要がある。

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Published: 2025-01-30  

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