P03-14
Recent Developments of FMODB in 2024: Efforts Towards Utilization of FMO data
Kikuko KAMISAKA *1, Chiduru WATANABE1, Daisuke TAKAYA2, Teruki HONMA1
1Center for Biosystems Dynamics Research, RIKEN
2Graduate School of Pharmaceutical Sciences, Osaka University
( * E-mail: kikuko.kamisaka@riken.jp )
Our group has been developing FMODB (https://drugdesign.riken.jp/FMODB/)[1], which has centrally managed the results of calculations using the fragment molecular orbital (FMO) method since 2017. FMO data and user numbers have steadily increased.
The FMO method, a type of quantum chemical calculation, is a technique that precisely analyzes the behavior of electrons and, through Pair Interaction Energy Decomposition Analysis (PIEDA), accurately handles dispersion forces, such as CH-π, π-π, and Cation-π interactions, enabling high-precision predictions of intermolecular and intramolecular interaction energies. FMODB provides researchers with the analysis results of this FMO method, creating an environment in which they can quickly access reliable data without having to perform calculations themselves. This improves research efficiency and enables more accurate interaction analysis.
Since 2024, FMODB has started collaborating with PDBj (https://pdbj.org/), which provides 3D structure information data on biopolymers obtained by structural biology experiments. Mutual links between entries registered in FMODB and PDBj have been established, thereby allowing researchers to access 3D structural information of biopolymers and detailed interaction energies based on those structures. An environment is being established for the mutual use of both databases. In addition, the Web API, which had been developed as a beta version, has been made public, allowing researchers and developers to access FMODB's calculation data through the API and use them in their research. This mutual collaboration and API release will promote the utilization of FMO data in structural biology and drug discovery research[2] enabling effective approaches to elucidate and deepen our understanding of molecular functions through FMO-based interaction analysis. Meanwhile, the BioStation Viewer software, which can visualize and analyze FMO calculation results, has added a function to directly load data from FMODB, making it even easier to use FMO calculation data. This presentation introduces the current status and recent efforts of FMODB as outlined above.
Acknowledgment
The authors thank Prof. Genji Kurisu and Dr. Gert-Jan Bekker of Osaka University for their support in collaborating with PDBj, as well as Dr. Kazumi Tsuda, Dr. Shu Koyama of Science & Technology Systems, Inc., and Mr. Akifumi Kato of Scorpion Tech LLC for technical support. This research was done as part of activities of the FMO Drug Design Consortium (https://fmodd.jp/top-en/) and was partially supported by Platform Project for Supporting Drug Discovery and Life Science Research (Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)) from AMED under Grant Number JP24ama121030. FMO calculations were performed using Fugaku (project IDs: hp240114 and ra000017).
[1] Takaya, D. et al., J. Chem. Inf. Model. 2021, 61, 2, 777–794.
[2] Watanabe, C. et al., J. Phys. Chem. Lett. 2023, 14, 15, 3609-3620.