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The 274th R-CCS Cafe (Dec 02, 2024)

Japanese
Details
Date Mon, Dec 02, 2024
Time 3:00 pm - 5:00 pm (3:00 pm - 3:40 pm Talks, 3:40 pm - 4:00 Discussions, 4:00 pm - 5:00 pm Free discussion and coffee break)
City Kobe, Japan/Online
Place

Lecture Hall (6th floor) at R-CCS, Online seminar on Zoom

  • If you are not affiliated with R-CCS and would like to attend R-CCS Cafe, please email us at r-ccs-cafe[at]ml.riken.jp.
Language Presentation Language: English
Presentation Material: English
Speakers

Ryo Kanada

HPC- and AI-driven Drug Development Platform Division
Senior Scientist

Teruki Honma

HPC- and AI-driven Drug Development Platform Division
Deputy Division Director

Talk Title and Abstract

Speaker: Ryo Kanada

Title:
Efficient All-Atom Structure Sampling via Parallelized Coarse-Grained Elastic Network Model and CG-to-AA Reconstruction
Abstract:
Efficient simulation of large-scale structural changes in target proteins is crucial for practical drug development. However, unbiased all-atom molecular dynamics (AA-MD) simulations often fail to capture long-timescale (ms-s) dynamics of large biomolecules due to computational limitations. Coarse-grained molecular dynamics (CG-MD), which simplifies each residue to a single degree of freedom, offers a computationally efficient alternative but lacks essential structural details, such as side chains, critical for drug design. To address these challenges, we developed a framework combining parallelized CG elastic network model (CG-ENM) sampling with efficient CG-to-AA reconstruction. This method enhances sampling coverage and restores atomic-level details required for detailed analysis. In this presentation, we will describe the methodology, performance improvements, and potential applications.

Speaker: Teruki Honma

Title:
FMODB: The World's First Database of Quantum Chemical Calculation for Biomacromolecules
Abstract:
The Fragment Molecular Orbital (FMO) method enables ab initio quantum chemical calculations for biomolecules such as proteins. By implementing the FMO method on Fugaku, we can rapidly obtain quantum chemical calculation results for numerous proteins, allowing us to construct and release the world's first database of quantum chemical calculation values for biomolecules, named FMODB. In the presentation, we will introduce the contents and applications of FMODB.

Important Notes

  • Please turn off your video and microphone when you join the meeting.
  • The broadcasting may be interrupted or terminated depending on the network condition or any other unexpected event.
  • The program schedule and contents may be modified without prior notice.
  • Depending on the utilized device and network environment, it may not be able to watch the session.
  • All rights concerning the broadcasted material will belong to the organizer and the presenters, and it is prohibited to copy, modify, or redistribute the total or a part of the broadcasted material without the previous permission of RIKEN.

（Nov 25, 2024）