Professor E. DEMET AKTEN (AKDOĞAN)
Head of the Department of Molecular Biology and Genetics
D BLOK 2. KAT 250
+90 (212) 5336532 - 1350
Education
Doctorate
UNIVERSITY OF AKRON (Akron, Ohio, U.S.A)
Polymer Science, Institute of Polymer Science
Master's Degree
Boğaziçi University
Chemical Engineering
Bachelor's Degree
Boğaziçi University
Chemical Engineering
Research Areas
- Molecular Modeling and Simulation
- Protein dynamics and function
- Allosteric Communication Pathways in Proteins
- Protein-Protein Interface Prediction
- Computer-Aided Drug Design
- Computational Structural Bioinformatics
- Membrane Proteins (GPCRs)
- Data Mining and Machine Learning Techniques
Work Experience
2020 /
Continuing
Kadir Has University
Professor
2014 /
2020
Kadir Has University
Associate Professor
2008 /
2014
Kadir Has University
Assistant Professor
2006 /
2008
Halic University
Assistant Professor
2002 /
2004
GNF (Genomics Institute of the Novartis Research Foundation)
Postdoctoral scholar
2001 /
2002
Carnegie Mellon University
Postdoctoral scholar
Publications
- Guner-Yılmaz, Ozde Zeynep; Kurkcuoglu, Ozge; Akten, Ebru Demet (2024), "Tunnel-like region observed as a potential allosteric site in Staphylococcus aureus Glyceraldehyde-3-phosphate dehydrogenase", Archives of Biochemistry and Biophysics, Vol.752, DOI: 10.1016/j.abb.2023.109875
- Turkmenoglu, Ipek; Kurtulus, Gamze; Sesal, Cenk; Kurkcuoglu, Ozge; Ayyildiz, Merve; Celiker, Serkan; Ozhelvaci, Fatih; Du, Xin; Liu, George Y.; Arditi, Moshe; Akten, Ebru Demet (2024), "Effective drug design screening in bacterial glycolytic enzymes via targeting alternative allosteric sites", Archives of Biochemistry and Biophysics, Vol.762, DOI: 10.1016/j.abb.2024.110190
- Celebi, Metehan; Akten, Ebru Demet (2022), "Altered Dynamics of S. aureus Phosphofructokinase via Bond Restraints at Two Distinct Allosteric Binding Sites", Journal of Molecular Biology, Vol.434, No.17, DOI: 10.1016/j.jmb.2022.167646
- Celebi, Metehan; Inan, Tugce; Kurkcuoglu, Ozge; Akten, Ebru Demet (2022), "Potential allosteric sites captured in glycolytic enzymes via residue-based network models: Phosphofructokinase, glyceraldehyde-3-phosphate dehydrogenase and pyruvate kinase", Biophysical Chemistry, Vol.280, DOI: 10.1016/j.bpc.2021.106701
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Sogunmez, Nuray; Akten, Ebru Demet (2022), "Information Transfer in Active States of Human β
2 -Adrenergic Receptor via Inter-Rotameric Motions of Loop Regions", Applied Sciences (Switzerland), Vol.12, No.17, DOI: 10.3390/app12178530 - Metin, Reyhan; Akten, Ebru Demet (2021), "Drug repositioning to propose alternative modulators for glucocorticoid receptor through structure-based virtual screening", Journal of Biomolecular Structure and Dynamics, DOI: 10.1080/07391102.2021.1960608
- Hu, Guang; Doruker, Pemra; Li, Hongchun; Akten (Akdoğan), Ebru Demet (2021), "Editorial: Understanding Protein Dynamics, Binding and Allostery for Drug Design", Frontiers in Molecular Biosciences, Vol.8, 681364 DOI: 10.3389/fmolb.2021.681364
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Sogunmez, Nuray; Akten, Ebru Demet (2020), "Distinctive communication networks in inactive states of β
2 -adrenergic receptor: Mutual information and entropy transfer analysis", Proteins: Structure, Function and Bioinformatics, Vol.88, No.11, 1458-1471 DOI: 10.1002/prot.25965 - Ayyildiz, Merve; Celiker, Serkan; Ozhelvaci, Fatih; Akten, E. Demet (2020), "Identification of Alternative Allosteric Sites in Glycolytic Enzymes for Potential Use as Species-Specific Drug Targets", Frontiers in Molecular Biosciences, Vol.7, DOI: 10.3389/fmolb.2020.00088
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Sogunmez, Nuray; Akten, E. Demet (2019), "Intrinsic Dynamics and Causality in Correlated Motions Unraveled in Two Distinct Inactive States of Human β
2 -Adrenergic Receptor", Journal of Physical Chemistry B, Vol.123, No.17, 3630-3642 DOI: 10.1021/acs.jpcb.9b01202 -
Dilcan, Gonca; Doruker, Pemra; Akten, Ebru Demet (2019), "Ligand-binding affinity of alternative conformers of human β
2 -adrenergic receptor in the presence of intracellular loop 3 (ICL3) and their potential use in virtual screening studies", Chemical Biology and Drug Design, Vol.93, No.5, 883-899 DOI: 10.1111/cbdd.13478 - Çifci, Gülşah; Aviyente, Viktorya; Akten, E. Demet; Monard, Gerald (2017), "Assessing protein–ligand binding modes with computational tools: the case of PDE4B", Journal of Computer-Aided Molecular Design, Vol.31, No.6, 563-575 DOI: 10.1007/s10822-017-0024-7
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Ozgur, Canan; Doruker, Pemra; Akten, E. Demet (2016), "Investigation of allosteric coupling in human β
2 -adrenergic receptor in the presence of intracellular loop 3", BMC Structural Biology, Vol.16, No.1, DOI: 10.1186/s12900-016-0061-9 - Özyiǧit, Ibrahim Ethem; Akten, E. Demet; Pekcan, Önder (2016), "Structural analysis of peptide fragments following the hydrolysis of bovine serum albumin by trypsin and chymotrypsin", Journal of Biomolecular Structure and Dynamics, Vol.34, No.5, 1092-1100 DOI: 10.1080/07391102.2015.1068712
- Kurkcuoglu, Zeynep; Findik, Doga; Akten, Ebru Demet; Doruker, Pemra (2015), "How an Inhibitor Bound to Subunit Interface Alters Triosephosphate Isomerase Dynamics", Biophysical Journal, Vol.109, No.6, 1169-1178 DOI: 10.1016/j.bpj.2015.06.031
- Koroglu, Ayca; Akten, Ebru Demet (2015), "Transmembrane helix 6 observed at the interface of β 2AR homodimers in blind docking studies", Journal of Biomolecular Structure and Dynamics, Vol.33, No.7, 1503-1515 DOI: 10.1080/07391102.2014.962094
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Yakar, Ruya; Akten, Ebru Demet (2014), "Discovery of high affinity ligands for β
2 -adrenergic receptor through pharmacophore-based high-throughput virtual screening and docking", Journal of Molecular Graphics and Modelling, Vol.53, 148-160 DOI: 10.1016/j.jmgm.2014.07.007 -
Ozcan, Ozer; Uyar, Arzu; Doruker, Pemra; Akten, Ebru Demet (2013), "Effect of intracellular loop 3 on intrinsic dynamics of human β
2 -adrenergic receptor", BMC Structural Biology, Vol.13, No.1, DOI: 10.1186/1472-6807-13-29 - Çakan, Sibel; Akdoğan, Ebru Demet (2013), "Exploring distinct binding site regions of β2 -adrenergic receptor via coarse-grained molecular dynamics simulations", Turkish Journal of Chemistry, Vol.37, 449-463 DOI: 10.3906/kim-1208-16
- Çifci, Gülşah; Aviyente, Viktorya; Akten, E. Demet (2012), "Molecular docking study based on pharmacophore modeling for novel phosphodiesteraseIV inhibitors", Molecular Informatics, Vol.31, No.6-7, 459-471 DOI: 10.1002/minf.201100141
- Akten (Akdoğan), E. Demet; Erman, Burak; Yelekci, Kemal (2011), "In silico design of novel and highly selective lysine-specific histone demethylase inhibitors", Turkish Journal of Chemistry, Vol.35, 523-542 DOI: 10.3906/kim-1102-985
- Kürkçüoğlu, Zeynep; Ural, Gulgun; Akten (Akdoğan), Ebru Demet; Doruker, Pemra (2011), "Blind Dockings of Benzothiazoles to Multiple Receptor Conformations of Triosephosphate Isomerase from Trypanosoma cruzi and Human", Molecular Informatics, Vol.30, 986-995 DOI: 10.1002/minf.201100109
- Akten, E. Demet; Cansu, Sertan; Doruker, Pemra (2009), "A docking study using atomistic conformers generated via elastic network model for cyclosporin a/cyclophilin a complex", Journal of Biomolecular Structure and Dynamics, Vol.27, No.1, 13-25 DOI: 10.1080/07391102.2009.10507292
Projects
| Project Name | Role in the Project | Project Type | Fund Establishment | Project Date |
|---|---|---|---|---|
| Protein Kompleks Arayüzey Bölgelerin Yapısal Parmak İzleri: Makine Öğrenme Yöntemiyle Arayüzey Tahmini | Yürütücü | Ulusal Proje | TÜBİTAK ARDEB |
01.03.2022 01.03.2025 |
| Glikolitik enzimlerde türe özgü bağlanma bölgelerinin belirlenmesi ve allosterik ilaç tasarımında kullanımı | Yürütücü | Ulusal Proje | TÜBİTAK ARDEB |
01.03.2019 01.03.2022 |
| 118F412: Sonlu Metrik Uzayların Gromov Çarpımları ile İncelenmesi ve Filogenetik Uygulamaları | Araştırmacı (Yürütücü: Prof. Dr. Ayşe Hümeyra Bilge) | Ulusal Proje | TÜBİTAK ARDEB 1001 |
01.03.2019 01.03.2021 |
| Kompleks Proteinlerin Farklı Bölgelerindeki Amino Asit Dağılımı ve Etkileşimini Etkileyen Çevresel ve Yapısal Faktörlerin İncelenmesi: Hücre Zarı Ortamı, Sekonder Yapı ve Kompleks Yapıdaki Mo | Yürütücü | Ulusal Proje | TÜBİTAK ARDEB |
01.09.2019 01.09.2020 |
| 213M544- b2 Adrenerjik Reseptöründe Aktif ve İnaktif Hallere Geçişlerdeki Allosterik Mekanizmanın Araştırılması ve İlaç Tasarım Çalışmalarında Uygulaması | Yürütücü | Ulusal Proje | TÜBİTAK ARDEB |
01.04.2014 01.04.2017 |
| 113M237: New computational approaches to unravel allosteric mechanisms and ligand binding sites | Araştırmacı (Yürütücü: Prof. Dr. Pemra Doruker) | Ulusal Proje | TÜBİTAK ARDEB 1001 |
01.03.2013 01.03.2016 |
| 109M281: Beta-2 Adrenerjik Reseptör Proteinin Dinamik Yapısının Araştırılması ve Bilgisayar Destekli İlaç Tasarımındaki Önemi | Yürütücü | Ulusal Proje | TÜBİTAK ARDEB |
01.11.2009 01.11.2012 |
| 109M213: Development and application of hybrid algorithms for studying protein flexibility and conformational transitions | Araştırmacı (Yürütücü: Prof. Dr. Pemra Doruker) | Ulusal Proje | TÜBİTAK ARDEB 1001 |
01.09.2009 01.09.2012 |
Courses Offered
| Course Name | Course Code | Period |
|---|---|---|
| Graduate Project II | MBG412 | 2023/24 Spring |
| Methods in Structural Biology | MBG408 | 2023/24 Spring |
| Computer Aided Drug Design | MBG432 | 2023/24 Spring |
| Introduction to Bioinformatics | MBG304 | 2023/24 Spring |
| Proteins in Action | MBG429 | 2023/24 Fall |
| Bioinformatics I | BGE203 | 2023/24 Fall |
| Proteins in Motion | CSE605 | 2023/24 Fall |
| Graduate Project I | MBG411*1 | 2024/25 Fall |
| General Chemistry Lab I | CHEM121 | 2024/25 Fall |
| Molecular Modeling and Simulation | MBG320 | 2024/25 Fall |