Limited to 30 people.
Date: October 14, 2024
Event Type: Training
Format: Face-to-face (Sabancı University- Altunizade Digital Campus, İstanbul)
Topic: Computational Biology
Overview: This one-day event is to be delivered by Dr. Canan Atilgan and Dr. Melike Berksöz from Sabanci University. The training will consist of a morning theory session and an afternoon practice session. The theory session will cover the basics of how genetically encoded fluorescent biosensors work and what some common design challenges are. In the afternoon, we will continue with hands-on sessions including using visualization and analysis of some biosensors reported in the literature. The workshop aims to train the attendees on using AlphaFold2 to design chimeric proteins, model the intricacies of the chromophore environment, and provide the kind of analyses to be performed on the MD simulations carried out on these systems. Experimental molecular biologists who are interested in implementing computational protein design into their research are welcome.
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
Prerequisite(s): Participants are expected to have a knowledge of protein structure and minimal experience with molecular dynamics simulations.
About the instructor:
Canan Atılgan:
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 served as its President during the 2021-24 term. She is an elected member of EMBO and Academia Europaea.
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/
Melike Berksöz:
Melike Berksöz received her BS degree in Chemistry from Middle East Technical University in 2010 and her MS degree from Albert Ludwigs Universität Freiburg in 2015. During her graduate studies, she worked on structural and functional characterization of bacterial membrane ion transporters. After returning to Turkey, she started working at a private biotech R&D laboratory and engaged in development of chromatography and mass spectrometry methods to characterize potential therapeutic antibodies. She completed her PhD in MIDST lab under the supervision of Prof. Canan Atılgan. Her dissertation focused on understanding allosteric mechanisms that govern the chromophore environment in fluorescent biosensors which can guide the design of novel sensing agents aganist desired ligands.
Moderator: Dr. Canan Atılgan
Application Due: October 13, 2024
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.
Acknowledgments
This event has been supported by TUBITAK project number 121Z329 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.
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
