Tutorials

Yoshihiro UESAWA（Meiji Pharmaceutical University）
Tsuyoshi ESAKI（Shiga University）

◆Registration
https://forms.gle/5B51XrgeAMuvthdRA

The FMO database (FMODB; https://drugdesign.riken.jp/FMODB/), which contains fragment molecular orbital (FMO) calculation results, has increased the number of data since its public release in February 2019 and as of July 29, 2024, utilizing supercomputers such as Fugaku 37426 FMO computed data (unique PDB ID: 7782) have been released. Recently, approaches such as feature extraction of interaction energy and AI prediction have started as information life science approaches utilizing FMO data. In this session, we will present an overview of FMODB for users who are considering starting FMO calculations. Using actual, registered data, we will also introduce analysis methods and the latest research cases for drug discovery research. In this process, users will experience how to analyze actual FMO calculations in a tutorial format. We look forward to your participation if you would like to learn more about FMODB and analyze actual FMO calculation results.

Chiduru WATANABE (RIKEN)
Koichiro KATO (Kyushu University)
Shuhei MIYAKAWA（Osaka University）

◆Program

(1) 13:00-13:05 Introduction
    Shuhei Miyakawa (Osaka University)

(2) 13:05-14:35 Introduction to the FMO database and how to use the data
    Chiduru Watanabe (RIKEN BDR)

Interaction energies (IFIE/PIEDA) obtained by the FMO method, one of the quantum chemical calculations, are expected to be applied to protein-ligand interaction analysis and drug discovery research. Our group has developed the FMODB to accumulate FMO calculation data. It provides a simple web interface to view FMO data calculated by members of the FMODD consortium and an automated FMO calculation protocol. This section introduces the functions provided by the FMODB web interface and its development status. We also plan to demonstrate data retrieval by setting various conditions, such as structural information of target proteins and modeling methods, to utilize FMODB data with a complete set of calculation conditions.

(3) 14:35-14:55 Break

(4) 14:55-16:25 Interaction clustering analysis for FMODB data
    Ruri Mihata (Osaka University)

Interaction energy (IFIE/PIEDA) analysis will be performed by BioStation Viewer, using the calculated results of the estrogen receptor (ER) β complex published in FMODB as an example. Then, practice analysis the Visualized Cluster Analysis of Protein-Ligand-Interaction (VISCANA) function for multiple complex structures. To extract features in ligand-receptor binding, we will perform cluster analysis of ligands based on interaction energies with amino acid residues by VISCANA.

(5) 16:25-16:35 Summary
    Koichiro Kato (Kyushu University)

(6) 16:35-17:00 Individual consultation

◆Registration
https://forms.gle/BTQsdTi18heGEnRU9

Applicants wishing to participate in this tutorial must register for the CBI conference. If you are unable to make it after registering, please contact the FMODB Tutorial Office (fmo_cbi2024@mail.cstm.kyushu-u.ac.jp) in advance. The tutorials have limited seating, and we ask for your cooperation in ensuring that as many people as possible who wish to participate are able to do so.

◆Preparation in advance

In parallel with the tutorial, you will operate the FMO database and BioStation Viewer. The latest version of BioStation Viewer and other programs and data to be used in the tutorial will be posted on the website shown in the following "FMODB Tutorial Documents" about one week before the tutorial.

◆FMODB Tutorial Documents
https://drugdesign.riken.jp/pub/CBI2024tut/

Takayuki SERIZAWA (Daiichi Sankyo Company, Limited)

https://peatix.com/event/4046509/view
https://github.com/cbi-society/cheminfo_tutorial_20241028_pub/