Limited to 25 people.
Date: March 27, 2026
Event Type: Training
Format: Face-to-face (Sabancı University- Altunizade Digital Campus, İstanbul)
Topic: Computational Biology
Overview:
In the theory session, we will introduce the transition from atomistic molecular dynamics simulations to coarse-grained (CG) models and discuss how coarse-graining enables accession to longer time and larger length scales. The session will include an overview of the Martini force field, basic mapping strategies, and the use of GROMACS for the system setup and simulation. An introduction to ligand parameterization within the Martini framework will also be provided.
In the hands-on session, participants will set up and run coarse-grained simulations using GROMACS. Practical exercises will include trajectory analysis, dynamics evaluation, and an introduction to backmapping from coarse-grained to atomistic resolution.
Agenda: The training will consist of two sections: morning and afternoon sessions. Registration will start at 9:30 AM, and the first session will begin at 10:00 AM.
Level: Intermediate
Language: English
Duration: 6 Hours
Target Audience: Academia
Prerequisite(s): Basic familiarity with molecular dynamics and working in Linux environment is recommended. Prior experience with coarse-grained simulations is not required.
About the instructor:
Özge Şensoy received her B.Sc. degrees in Molecular Biology and Genetics and Chemistry from İstanbul Technical University in 2005. She completed her M.Sc. and Ph.D. at Koç University, where she focused on protein dynamics for development of peptide-based materials. She carried out her postdoctoral research at Weill Cornell Medical College between 2011 and 2015. Since 2015, she has been a faculty member in the Department of Biomedical Engineering at İstanbul Medipol University. Her research centers on the structural and dynamic mechanisms underlying biased G protein–coupled receptor signaling, RAS protein dynamics, posttranslational modifications and antibiotic resistance. Using computational approaches, she aims to understand how small therapeutic molecules modulate protein dynamics and signaling pathways, with the goal of development of targeted therapeutic strategies.
Moderator: Dr. Canan Atılgan
Application Due: March 27, 2026
Contact: ncc@ulakbim.gov.tr
This course is offered free of charge
Notes:
Registration based on the principle of "first come – first served"
Please cancel your registration if you won't be able to attend so that others may attend.
Participants will use their own laptop or computer for the hands-on session.
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Disclaimer
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Acknowledgments
This event is supported by the EuroCC 2 and EuroCC4SEE projects, which received funding from the European High-Performance Computing Joint Undertaking (JU) under grant agreements No. 101101903 and No. 101191697, respectively. The JU receives support from the Digital Europe Programme and Germany, Bulgaria, Austria, Croatia, Cyprus, Czech Republic, Denmark, Estonia, Finland, Greece, Hungary, Ireland, Italy, Lithuania, Latvia, Poland, Portugal, Romania, Slovenia, Spain, Sweden, France, Netherlands, Belgium, Luxembourg, Slovakia, Norway, Türkiye, Republic of North Macedonia, Iceland, Montenegro, Serbia.
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