Limited to 25 people.
Date: November 30, 2025
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 fundamentals of molecular dynamics (MD) simulations of membrane proteins and focus on the principles of steered molecular dynamics (SMD), including how external forces are applied to explore conformational changes or molecular transport through biological channels. We will discuss how to set up protein–membrane systems and how to interpret SMD force profiles and potential of mean force (PMF) results. In the hands-on session, we will perform MD and SMD simulations of a membrane-embedded protein to observe the passage of a small molecule through the pore. The exercises will include system building, equilibration, and analysis using CHARMM-GUI, NAMD, and VMD software.
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): Participants are expected to have a knowledge of protein structure and experience with molecular dynamics simulations.
About the instructor:
Işık Kantarcioglu finished her B.Sc. in Genetics and Bioengineering at Istanbul Bilgi University in 2015. She then pursued an M.Sc. in Bioengineering at Bahcesehir University, graduating in 2018, with a thesis focused on computational approaches to discover novel inhibitors. In 2024, Işık earned her Ph.D. from Sabanci University, where her research centered on the TolC transmembrane efflux protein. She utilized both computational and experimental methods to reveal how TolC’s structural shifts enhance its ability to expel β-lactam antibiotics, aiming to understand the resistance mechanisms. Işık conducted her experiments at UTSW Medical Center in collaboration with Toprak Lab, supported by TÜBİTAK funding for a year. As a postdoctoral researcher at MIDST Lab, she plans to expand her research to investigate other efflux pumps and their roles in antibiotic resistance, advancing our understanding of bacterial defense mechanisms against a broader spectrum of antibiotics.
Moderator: Dr. Canan Atılgan
Application Due: November 30, 2025
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.
-------
Disclaimer
Sadece EuroHPC JU katılımcı ülkelerinde (Türkiye gibi) yaşayan ve çalışan katılımcılar etkinliğe katılım sağlayabilir.( https://eurohpc-ju.europa.eu/about/discover-eurohpc-ju_en)
Yalnızca resmi e-posta adresleri (çalıştığınız kurum e-posta adresi veya edu uzantılı üniversite e-posta adresleri) kayıt için kabul edilmektedir; kişisel veya jenerik e-posta adresleri (gmail, hotmail, yahoo gibi) kabul edilmemektedir.
------
Bizi X ve LinkedIn hesaplarımızdan takip edebilirsiniz. YouTube kanalımıza abone olmayı unutmayın!
- Twitter: https://twitter.com/EuroCC_Turkey
- LinkedIN: https://www.linkedin.com/company/eurocc-turkey
- YouTube: https://www.youtube.com/c/EuroCCTurkey
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.
Follow us on Twitter and LinkedIn. Subscribe to our YouTube Channel
https://twitter.com/EuroCC_Turkey
https://www.linkedin.com/company/eurocc-turkey
https://www.youtube.com/channel/UC-qaWnbbTl6OPiPasUf4t8w/playlists
