TOP Events & Outreach R-CCS Cafe The 274th R-CCS Cafe (Dec 02, 2024)
The 274th R-CCS Cafe (Dec 02, 2024)
JapaneseDate | Mon, Dec 02, 2024 |
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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
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Language | Presentation Language: English Presentation Material: English |
Speakers |
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
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(Nov 25, 2024)