Limited to 30 people.
Date: March 20, 2024
Format: Face-to-face (Sabancı University- Altunizade Campus, İstanbul)
Topic: Computational Biology
Overview: This one-day event is to be delivered by Canan Atilgan from Sabanci University. The morning session will be devoted to the theory of a general overview of advanced techniques for the conformational search of proteins. The issue of collective variables will also be addressed in some detail. We will then focus on the theory behind the metadynamics (MetaD) technique. In the afternoon, we will hold a hands-on session on setting up and running a MetaD simulation. We will finally focus on the analysis of the outputs and discuss best practices.
Agenda: The training will consist of two sections: theory and hands-on sessions. Registration will start at 9:00 AM, and the first session will begin at 9:30 AM.
Level: Intermediate
Language: English
Duration: 7 Hours
Target Audience: Academia
Prerequisites: Participants are expected to have minimal experience with MD simulations of proteins or similar systems
- Familiarity with a programming language, preferably Python
- Familiarity with molecular dynamics software, preferably NAMD
About the instructor:
Canan Atılgan received her BS degree from the Department of Chemical Engineering of Boğaziçi University in 1991, and her PhD degree from the same institution in 1996. She was a postdoctoral research fellow at the Supercomputer Computations Research Institute of Florida State University through 1999. Since then, she has been a faculty member at the Faculty of Engineering and Natural Sciences of Sabancı University. She is the recipient of Boğaziçi University PhD Thesis (1996), TÜBİTAK Encouragement (2002), Turkish Academy of Sciences Young Scientist (2004), L’Oréal Turkey For Women in Science (2005) Awards. She is an elected member of Bilim Akademisi - Science Academy, Turkiye and is its current President. She is an elected member of EMBO and Academia Europaea. She currently serves as Biophysical Society’s Ambassador to Turkey.
Dr. Atılgan’s expertise is on the computational and theoretical investigation of complex molecules. Her focus is on disclosing dynamical features of soft matter systems that lead to unique behavior identified, but not explained, through experiments. Protein dynamics, manipulation of protein conformations, understanding the antibiotic resistance problem at the scale of the three-dimensional structure of single proteins are areas of current interest for her.
http://people.sabanciuniv.edu/canan/
Contact: ncc@ulakbim.gov.tr
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 with preinstalled NAMD/VMD during the hands-on session.
Acknowledgments
This event has been supported by TUBITAK project number 122F149 and EuroCC 2 project number 101101903. The EuroCC 2 project has received funding from the European High-Performance Computing Joint Undertaking (JU) under grant agreement No 101101903. 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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