Invitation to attend BMMP Online Seminar Series (30th September 2025 9:30AM)

[Ragothaman Yennamalli]

Dear All,

Biomolecular and Materials Modelling Platform (Online) of India (bm-mp.in) is delighted to invite you to an exciting seminar in 2025.

Please find the flyer and the abstract attached in the pdf. The seminar will be delivered by an expert in protein ligand docking: Prof. Suyong Re from National Institutes of Biomedical Innovation, Health and Nutrition (NIBN), Japan

Details of the Seminar:
Title: Protein-ligand dynamic docking using molecular dynamics simulation
Date: 30 September 2025, Tuesday 
Time: 9:30-10:30 AM (India Standard Time)
Format: ZOOM: https://shorturl.at/mrqPw (Meeting ID: 676 7637 3293
Passcode: 559215)

Please find the abstract below. We look forward to your participation in what promises to be an enlightening and engaging session. Please share them among your students and encourage them to participate.

Protein-ligand dynamic docking using molecular dynamics simulation
Understanding how proteins recognize and bind to ligands is fundamental to many biological processes, including drug action. Our current understanding of ligand recognition mostly comes from static structures of bound complexes determined by X-ray crystallography. However, recent advances in drug discovery highlight the importance of not only how tightly a drug binds, but also how long it stays bound, referred to as residence time. To study dynamic aspects of protein-ligand binding, molecular dynamics (MD) simulations are useful, as they allow the motion of biomolecules over time to be visualized at atomic resolution. However, conventional MD simulations are limited in that they rarely capture full binding or unbinding events, even on the world’s fastest supercomputers. In this talk, we introduce enhanced MD methods based on replica-exchange techniques that overcome these limitations. One such method, called generalized replica exchange with solute tempering (gREST) [1], allows us to predict whether a ligand molecule will bind or not based on the free energy landscape [2]. An extension of this method, 2D-gREST/REUS, combines gREST with another technique called umbrella sampling. This approach makes it possible to observe multiple binding modes and the pathways connecting them, which are rarely captured in experiments [3]. These advanced simulations provide insights into the key factors that govern binding and unbinding processes, offering valuable guidance for designing more effective drug compounds.
[1] Kamiya et al. J. Chem. Phys. 2018, 149, 072304. [1] Niitsu, Re et al. J. Chem. Inf. Model. 2019, 59, 3879-3888. [3] Re et al. Proc. Natl. Acad. Sci. 2019, 116, 18404-18409.

Thanks and Regards,
BMMP-India Governance Team

Governance Team and Affiliations:
1. Durba Sengupta, Scientist, National Chemical Laboratory (CSIR), India.
2. Neha Sureshchandra Gandhi, Adjunct professor, Queensland University of Technology

3. Ragothaman Yennamalli, Senior Assistant Professor, School of Chemical & Biotechnology, SASTRA University.
4. Aditya Kumar Padhi, Assistant Professor, School of Biochemical Engineering, IIT (BHU), Varanasi.
4. Rajnish, Assistant Professor, Department of Pharmaceutical Engineering and Technology, IIT (BHU), Varanasi.
6. Prakash Muthuramalingamu, Research Professor & Head, Department of Chemistry, SRMIST, Kattankulathur, Chennai.

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Ragothaman M Yennamalli, Ph.D.

Senior Assistant Professor,

Department of Bioinformatics,

School of Chemical and Biotechnology,

SASTRA University,

Thanjavur, India

https://yennamalli-lab.in/

Chair, Publications Committee, ISCB

Executive Committee Member, APBioNet

Associate Editor, Computational and Structural Biotechnology Journal

Associate Editor, Bioinformatics and Biology Insights

Special Issue Editor, Biophysical Journal

Editorial Board, BMC Bioinformatics

Editorial Board, Scientific Reports

Early Career Researcher Review Board, Protein Science

"When you can do the common things of life in an uncommon way, you will command the attention of the world." -George Washington Carver
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