Professor
E. DEMET AKTEN (AKDOĞAN)
Head of the Department of Molecular Biology and Genetics
D BLOK 2. KAT 250
+90 (212) 533 65 32 / 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
-
"Hydrogels from Protein–Polymer Conjugates: A Pathway to Next-Generation Biomaterials",
Alayoubi, Oubadah; Poyraz, Yağmur; Hassan, Gana; Gül, Sümeyye Berfin; Çalhan, Nergiz; Mert Şahin, Naz Mina; Gautam, Megha; Kutlu, Aylin; Özuğur Uysal, Bengü; Akten, Ebru Demet; Pekcan, Önder; Gels, (2025) Vol.11, No.2, DOI: 10.3390/gels11020096 -
"Tunnel-like region observed as a potential allosteric site in Staphylococcus aureus Glyceraldehyde-3-phosphate dehydrogenase",
Guner-Yılmaz, Ozde Zeynep; Kurkcuoglu, Ozge; Akten, Ebru Demet; Archives of Biochemistry and Biophysics, (2024) Vol.752, DOI: 10.1016/j.abb.2023.109875 -
"Effective drug design screening in bacterial glycolytic enzymes via targeting alternative allosteric sites",
Turkmenoglu, Ipek; Kurtulus, Gamze; Sesal, Cenk; Kurkcuoglu, Ozge; Ayyildiz, Merve; Celiker, Serkan; Ozhelvaci, Fatih; Du, Xin; Liu, George Y.; Arditi, Moshe; Akten, Ebru Demet; Archives of Biochemistry and Biophysics, (2024) Vol.762, DOI: 10.1016/j.abb.2024.110190 -
"Altered Dynamics of S. aureus Phosphofructokinase via Bond Restraints at Two Distinct Allosteric Binding Sites",
Celebi, Metehan; Akten, Ebru Demet; Journal of Molecular Biology, (2022) Vol.434, No.17, DOI: 10.1016/j.jmb.2022.167646 -
"Potential allosteric sites captured in glycolytic enzymes via residue-based network models: Phosphofructokinase, glyceraldehyde-3-phosphate dehydrogenase and pyruvate kinase",
Celebi, Metehan; Inan, Tugce; Kurkcuoglu, Ozge; Akten, Ebru Demet; Biophysical Chemistry, (2022) Vol.280, DOI: 10.1016/j.bpc.2021.106701 -
"Information Transfer in Active States of Human β
2 -Adrenergic Receptor via Inter-Rotameric Motions of Loop Regions",
Sogunmez, Nuray; Akten, Ebru Demet; Applied Sciences (Switzerland), (2022) Vol.12, No.17, DOI: 10.3390/app12178530 -
"Drug repositioning to propose alternative modulators for glucocorticoid receptor through structure-based virtual screening",
Metin, Reyhan; Akten, Ebru Demet; Journal of Biomolecular Structure and Dynamics, (2021) DOI: 10.1080/07391102.2021.1960608 -
"Editorial: Understanding Protein Dynamics, Binding and Allostery for Drug Design",
Hu, Guang; Doruker, Pemra; Li, Hongchun; Akten (Akdoğan), Ebru Demet; Frontiers in Molecular Biosciences, (2021) Vol.8, 681364 DOI: 10.3389/fmolb.2021.681364 -
"Distinctive communication networks in inactive states of β
2 -adrenergic receptor: Mutual information and entropy transfer analysis",
Sogunmez, Nuray; Akten, Ebru Demet; Proteins: Structure, Function and Bioinformatics, (2020) Vol.88, No.11, 1458-1471 DOI: 10.1002/prot.25965 -
"Identification of Alternative Allosteric Sites in Glycolytic Enzymes for Potential Use as Species-Specific Drug Targets",
Ayyildiz, Merve; Celiker, Serkan; Ozhelvaci, Fatih; Akten, E. Demet; Frontiers in Molecular Biosciences, (2020) Vol.7, DOI: 10.3389/fmolb.2020.00088 -
"Intrinsic Dynamics and Causality in Correlated Motions Unraveled in Two Distinct Inactive States of Human β
2 -Adrenergic Receptor",
Sogunmez, Nuray; Akten, E. Demet; Journal of Physical Chemistry B, (2019) Vol.123, No.17, 3630-3642 DOI: 10.1021/acs.jpcb.9b01202 -
"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",
Dilcan, Gonca; Doruker, Pemra; Akten, Ebru Demet; Chemical Biology and Drug Design, (2019) Vol.93, No.5, 883-899 DOI: 10.1111/cbdd.13478 -
"Assessing protein–ligand binding modes with computational tools: the case of PDE4B",
Çifci, Gülşah; Aviyente, Viktorya; Akten, E. Demet; Monard, Gerald; Journal of Computer-Aided Molecular Design, (2017) Vol.31, No.6, 563-575 DOI: 10.1007/s10822-017-0024-7 -
"Investigation of allosteric coupling in human β
2 -adrenergic receptor in the presence of intracellular loop 3",
Ozgur, Canan; Doruker, Pemra; Akten, E. Demet; BMC Structural Biology, (2016) Vol.16, No.1, DOI: 10.1186/s12900-016-0061-9 -
"Structural analysis of peptide fragments following the hydrolysis of bovine serum albumin by trypsin and chymotrypsin",
Özyiǧit, Ibrahim Ethem; Akten, E. Demet; Pekcan, Önder; Journal of Biomolecular Structure and Dynamics, (2016) Vol.34, No.5, 1092-1100 DOI: 10.1080/07391102.2015.1068712 -
"How an Inhibitor Bound to Subunit Interface Alters Triosephosphate Isomerase Dynamics",
Kurkcuoglu, Zeynep; Findik, Doga; Akten, Ebru Demet; Doruker, Pemra; Biophysical Journal, (2015) Vol.109, No.6, 1169-1178 DOI: 10.1016/j.bpj.2015.06.031 -
"Transmembrane helix 6 observed at the interface of β 2AR homodimers in blind docking studies",
Koroglu, Ayca; Akten, Ebru Demet; Journal of Biomolecular Structure and Dynamics, (2015) Vol.33, No.7, 1503-1515 DOI: 10.1080/07391102.2014.962094 -
"Discovery of high affinity ligands for β
2 -adrenergic receptor through pharmacophore-based high-throughput virtual screening and docking",
Yakar, Ruya; Akten, Ebru Demet; Journal of Molecular Graphics and Modelling, (2014) Vol.53, 148-160 DOI: 10.1016/j.jmgm.2014.07.007 -
"Effect of intracellular loop 3 on intrinsic dynamics of human β
2 -adrenergic receptor",
Ozcan, Ozer; Uyar, Arzu; Doruker, Pemra; Akten, Ebru Demet; BMC Structural Biology, (2013) Vol.13, No.1, DOI: 10.1186/1472-6807-13-29 -
"Exploring distinct binding site regions of β2 -adrenergic receptor via coarse-grained molecular dynamics simulations",
Çakan, Sibel; Akdoğan, Ebru Demet; Turkish Journal of Chemistry, (2013) Vol.37, 449-463 DOI: 10.3906/kim-1208-16 -
"Molecular docking study based on pharmacophore modeling for novel phosphodiesteraseIV inhibitors",
Çifci, Gülşah; Aviyente, Viktorya; Akten, E. Demet; Molecular Informatics, (2012) Vol.31, No.6-7, 459-471 DOI: 10.1002/minf.201100141 -
"In silico design of novel and highly selective lysine-specific histone demethylase inhibitors",
Akten (Akdoğan), E. Demet; Erman, Burak; Yelekci, Kemal; Turkish Journal of Chemistry, (2011) Vol.35, 523-542 DOI: 10.3906/kim-1102-985 -
"Blind Dockings of Benzothiazoles to Multiple Receptor Conformations of Triosephosphate Isomerase from Trypanosoma cruzi and Human",
Kürkçüoğlu, Zeynep; Ural, Gulgun; Akten (Akdoğan), Ebru Demet; Doruker, Pemra; Molecular Informatics, (2011) Vol.30, 986-995 DOI: 10.1002/minf.201100109 -
"A docking study using atomistic conformers generated via elastic network model for cyclosporin a/cyclophilin a complex",
Akten, E. Demet; Cansu, Sertan; Doruker, Pemra; Journal of Biomolecular Structure and Dynamics, (2009) Vol.27, No.1, 13-25 DOI: 10.1080/07391102.2009.10507292
Projects
| Project Name | Role in the Project | Project Type | Fund Establishment | Start Date | End Date |
|---|---|---|---|---|---|
| "Bakteri ve parazit türlerine ait glikolitik enzimlerde türe özgü ilaç tasarımında kullanılacak hedef potansiyel allosterik bölgelerin belirlenmesi " | Yürütücü | Ulusal Proje | Diğer Ulusal |
27.12.2024 |
27.12.2025 |
| "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 |
| "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 |
| "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 |
Courses Offered
| Course Name | Course Code | Period |
|---|---|---|
| General Chemistry Lab II | CHEM122 | 2024/25 Spring |
| Scientific Research I | FENS495 | 2024/25 Spring |
| Introduction to Bioinformatics | MBG304 | 2024/25 Spring |
| Computer Aided Drug Design | MBG432 | 2024/25 Spring |
| Graduate Project I | MBG411*1 | 2024/25 Fall |
| General Chemistry Lab I | CHEM121 | 2024/25 Fall |
| Molecular Modeling and Simulation | MBG320 | 2024/25 Fall |