Developments and Activities in FMODB up to 2025: A Release Note

The fragment molecular orbital (FMO) method enables quantum chemical evaluation of intra- and intermolecular interactions in biomacromolecules at the fragment level. To facilitate data reuse and advance research in structural biology and drug discovery, we have developed the FMO database (FMODB, URL: https://drugdesign.riken.jp/FMODB/), which currently contains 77,277 entries. In this paper, we summarize the key features added to FMODB since 2021, including advanced search capabilities, enhanced interfragment interaction energy (IFIE) analysis tools, a batch IFIE analysis module, a Web API, and cross-links to PDBj. These updates markedly enhance usability and interoperability, thereby enabling more effective application of FMO data.

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Publication Details

Journal
Chem-Bio Informatics Journal
Published
2025-12-14
DOI
https://doi.org/10.1273/cbij.25.130
Primary Topic
Computational Drug Discovery Methods
Type
article
Field-Weighted Citation Impact
0.00

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article

Developments and Activities in FMODB up to 2025: A Release Note

Kazumi Tsuda, Tatsuya Ohyama, S. Koyama, Teruki Honma et al.
Chem-Bio Informatics Journal
Computational Drug Discovery Methods
article

Developments and Activities in FMODB up to 2025: A Release Note

Kazumi Tsuda, Tatsuya Ohyama, S. Koyama, Teruki Honma, Kikuko Kamisaka, Daisuke Takaya, Koichiro Kato, Chiduru Watanabe, Kaori Fukuzawa, Akifumi Kato, T. Isobe, Daisuke Murayama
article en

Abstract

The fragment molecular orbital (FMO) method enables quantum chemical evaluation of intra- and intermolecular interactions in biomacromolecules at the fragment level. To facilitate data reuse and advance research in structural biology and drug discovery, we have developed the FMO database (FMODB, URL: https://drugdesign.riken.jp/FMODB/), which currently contains 77,277 entries. In this paper, we summarize the key features added to FMODB since 2021, including advanced search capabilities, enhanced interfragment interaction energy (IFIE) analysis tools, a batch IFIE analysis module, a Web API, and cross-links to PDBj. These updates markedly enhance usability and interoperability, thereby enabling more effective application of FMO data.

Chem-Bio Informatics JournalVol. 25(0)
Kyushu University (JP), Scorpion Therapeutics (United States) (US), Systems Technology (United States) (US), RIKEN Center for Integrative Medical Sciences (JP), Systems and Technology Research (United States) (US), Osaka University of Pharmaceutical Sciences (JP)
Japan Agency for Medical Research and Development, National Institute of Advanced Industrial Science and Technology, Rikkyo University, Chiba University, Hoshi University, Japan Society for the Promotion of Science
Openalex Percentile: Top 61%
Computational Drug Discovery Methods
DOIOpen Access PDFOpenAlex
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