Demet yeni

Prof. Dr. E. Demet AKTEN AKDOĞAN


Address: Kadir Has University, Faculty of Natural Sciences and Engineering, Dept. Bioinformatics and Genetics, D Building, Room # 250.
Phone:      +90 212 533 65 32 / 1350
e-mail: or


bogazici B.S. Boğaziçi University – Chemical Engineering (1994)
bogazici  M.S. Boğaziçi University – Chemical Engineering  (1996)
Supervisor: Prof. Ivet Bahar
Akron   Ph.D   University of Akron – Polymer Science (2001)
Supervisor: Prof. Wayne L. Mattice


Academic Experience

carnegie mellon Post-doc: Carnegie Mellon University – Dept. of Chemical Engineering (2001-2002)
Supervisor: Prof. David S. Sholl
scripps Post-doc: Genomics Institute of the Novartis Research Foundation (GNF) / Scripps Research Institute (2002-2004)
Supervisor: Prof. Peter Schultz
halic Asst. Prof.: Haliç University – Dept of Molecular Biology and Genetics (2006-2008)
kadir has Asst. Prof.: Kadir Has University Dept of Bioinformatics and Genetics(2008 – 2013)
kadir has Assoc. Prof.: Kadir Has University Dept of Bioinformatics and Genetics (2013 – now)


Kadir Has University, Dean’s Rising Star Award for Faculty of Engineering and Natural Sciences in the Academic Year of 2011-2012

Courses Given 

2019-2020 Academic Year:

    • Bioinformatics I (BIO 203, Fall)
    • Bioinformatics II (BIO 204, Spring)
    • Computer-Aided Drug Design (BIO 510, Spring)
    • Computational Drug Design Techniques (BIO 610, Spring)


Past and Current Projects

tubitak TÜBİTAK-1001 (218M320). “Identification of species-specific regions in glycolytic enzymes and their use in allosteric drug design studies”. Project Director. Budget: 707.756,00 TL (2019-2022)
tubitak TÜBİTAK-1002 (119M188).Factors Affecting the Amino acid Propensity and Interactions in Interior, Surface and Interface Regions of Protein Complexes: Membrane Environment, Secondary Structure and Number of Monomer Units“. Project Director. Budget: 45.000,00 TL (2019-2020)
tubitak TÜBİTAK-1001 (213M544). “Investigating the Allosteric Mechanism in β2 Adrenergic Receptor upon Activation/Inactivation and its Application in Drug Design”. Project Director. Budget: 257,420 TL (2014-2016)
tubitak TÜBİTAK-1001 (113M237). “New computational approaches to unravel allosteric mechanisms and ligand binding sites”. Researcher (Project Director: Prof. Pemra Doruker Turgut). Budget: 238,000 TL (2013-2016)
tubitak TÜBİTAK-1001 (109M281). “Exploring the Dynamic Structure of β2 Adrenergic Receptor and its Importance in Computer-Aided Drug Design”. Project Director. Budget: 181,300 TL (2009-2012)
tubitak TÜBİTAK-1001 (109M213). “Development and application of hybrid algorithms for studying protein flexibility and conformational transitions”. Researcher (Project Director: Prof. Pemra Doruker Turgut). Budget: 234,145 TL (2009-2012)

Past Research Activities

bogazici Boğaziçi University, Polymer Research Center, “Effects of protein dynamics in computer-aided drug design”. Researcher, (2008)
scripps GNF Genomics Institute of the Novartis Research Foundations and the Scripps Research Institute, “Computer-aided drug design”. Postdoctoral scholar (2002-2004)
carnegie mellon Carnegie Mellon University, Chemical Engineering “Fully atomistic modeling and simulation of zeolites for the study of gas adsorption”. Postdoctoral scholar (2001-2002)
Akron University of Akron. Institute of Polymer Science, “Computer simulation and molecular modeling of polyolefins”. Research Assistant (1996-2001)
bogazici Boğaziçi University. Polymer Research Center, “Coarse-graned simulation and protein folding”. Research Assistant (1995-1996)

Recent Publications in SCI:

19. Sogunmez N, Akten ED, “Distinctive Communication Networks in Inactive States of  β2-Adrenergic Receptor: Mutual Information and Entropy Transfer Analysis”, Proteins: Structure, Function and Bioinformatics, 1-14 (2020)

18. Ayyildiz M, Celiker S, Ozhelvaci F, Akten ED, “Identification of Alternative Allosteric Sites in Glycolytic Enzymes for Potential Use as Species-Specific Drug Targets”, Frontiers in Molecular Biosciences, Vol 7, Article 88 (2020)

17. Sogunmez N, Akten ED, “Intrinsic Dynamics and Causality in Correlated Motions Unraveled in Two Distinct Inactive States of Human β2-Adrenergic Receptor”, J Phys Chem B, 123(17), 3630-3642 (2019)

16. Dilcan G, Doruker P, Akten ED, “Ligand-binding Affinity fo Alternative Conformers of Human β2-adrenergic Receptor in the Presence of Intracellular Loop 3 (ICL3) and their Potential Use in Virtual Screening Studies”, Chem Biol Drug Des, 1-17 (2019).

15. Cifci G, Aviyente V, Akten ED, Monard G, “Assessing protein-ligand binding modes with computational tools: the case of PDE4B”, J Comput Aided Mol Des, Vol: 31(6), 563-575 (2017).

14. Ozgur C, Doruker P, Akten ED, “Investigation of Allosteric Coupling in Human β2-adrenergic Receptor in the Presence of Intracellular Loop 3“, BMC Struct Biol, Vol:16, 9 (2016).

13. Ozyigit I, Akten ED, Pekcan O, “Structural Analysis of Peptide Fragments Following the Hydrolysis of Bovine Serum Albumin by Trypsin and Chymotrypsin“, J Biomol Str & Dyn, Vol: 34, pp:1092-1100 (2016)

12. Kurkcuoglu Z, Findik D, Akten ED, Doruker P, “How an inhibitor bound to subunit interface alters triosephosphate isomerase dynamics“, Biophysical J, Vol:109, pp:1169-1178 (2015)

11. Koroglu A, Akten ED, “Transmembrane helix 6 observed at the interface of β2AR homodimers in blind docking studies“, J Biomol Str & Dyn, Vol:33, pp:1503-1515 (2015)

10. Yakar R, Akten ED,Discovery of high affinity ligands for beta2 adrenergic receptor through pharmacophore-based high-throughput virtual screening and docking“. J Mol Graph & Model, Vol: 53, 148-160 (2014)

9. Ozcan O, Uyar A, Doruker P, Akten ED, “Effect of intracellular loop 3 on intrinsic dynamics of human beta-2 adrenergic receptor”. BMC Struct Biol, Vol:13, 29 (2013)

8. Cakan S, Akdoğan ED, “Exploring distinct binding site regions of beta-2 adrenergic receptor via coarse-grained molecular dynamics simulations”. Turkish J of Chem, Vol:35, 449-463 (2013)

7. Cifci G, Aviyente V, Akten ED,Molecular Docking Study Based on Pharmacophore Modeling for Novel PhosphodiesteraseIV Inhibitors”. Molecular Informatics, Vol:31, pp:459-471 (2012)

6. Kurkcuoglu Z., Ural G., Akten ED, Doruker P. “Blind Docking of Benzothiazoles to Multiple Receptor Conformations of Triosephosphate Isomerase from Trypanosoma cruzi and Human”. Molecular Informatics, Vol:30, pp:986-995 (2011)

5. Akdogan ED, Erman B, Yelekci Y, “In silico Design of Novel and Highly Selective Lysine-Specific Histone Demethylase Inhibitors”. Turkish J of Chem, Vol:35, 1-20 (2011)

4. Akten ED, Cansu S and Doruker P, “A Docking Study Using Atomistic Conformers Generated via Elastic Network Model for Cyclosporin A/Cyclophilin A Complex”. J Biomol Str & Dyn, Vol:27, pp:13-25 (2009)

3. Akten ED, Siriwardane, R., and Sholl, D., “Monte Carlo Simulation of Single- and Binary-Component Adsorption of CO2, N2, and H2 in Zeolite Na-4A”. Energy and Fuels, Vol:17, pp:977-983 (2003)

2. Goj A, Sholl D, Akten ED, and Kohen D, “Atomistic Simulation of CO2 and N2 Adsorption in Silica Zeolites: The Impact of Pore Size and Shape”. J Phys Chem B, Vol:106, pp:8367-8375 (2002)

1. Akten ED and Mattice WL “Monte Carlo Simulation of Head-to-Head, Tail-to-Tail Polypropylene and Its Mixing Behavior with Polyethylene in the Melt”. Macromolecules, Vol:34, pp:3389-3395 (2001)

Book Chapters

Rotational Isomeric State (RIS) Calculations, with and Illustrative Application to Head-to-Head, Tail-to-Tail Polypropylene” Chap 2. by Akten ED, Mattice WL, Suter UW in SIMULATION METHODS for POLYMERS, Edited by M. Kotelyanskii and DN Theodorou, 2004.

Theses Supervised

13. Reyhan Metin, Master’s Thesis. Kadir Has University, Computational Biology and Bioinformatics, advisor. “Investigating allosteric inhibitors for pyruvate kinase“, (2020-present)

12. Metehan Çelebi, Master’s Thesis. Kadir Has University, Computational Biology and Bioinformatics, advisor. “Identification of allosteric communication pathways in phosphofructokinase“, (2020-present)

11. Fatih Özhelvacı, Master’s Thesis. Boğaziçi University, Computational Science and Engineering, co-advisor. “Determination of Species-Specific Allosteric Binding Sites in Pyruvate Kinase and its Use in Drug Design Studies”. (2018-2020)

10. Serkan Çeliker, Master’s Thesis. Kadir Has University, Computational Biology and Bioinformatics, advisor. “Central Tunnel as an Alternative Allosteric Site in Glyceraldehyde-3-phosphate Dehydrogenase  for Potential Use as Species-Specific Drug Target“, (2018-2020)

9. Merve Ayyıldız, Master’s Thesis. Kadir Has University, Computational Biology and Bioinformatics, advisor.Identification of Species-Specific Regions in Phosphofructokinase and their Use in Allosteric Drug Design Studies“, (2018-2020)

8. Sercan Beytur. PhD Thesis. Kadir Has University, Bioinformatics and Genetics, advisor. Factors Affecting Protein-Protein Interfaces: Membrane Environment, Secondary Structure and Number of Monomer Units“, (2017-present)

7. Nuray Söğünmez. PhD Thesis. Kadir Has University, Bioinformatics and Genetics, advisor. “Identification of Distinct Communication Pathways in Human β2-Adrenergic Receptor via Molecular Dynamics Simulation (2016-2020)

6. Gonca Dilcan. Master’s Thesis. Kadir Has University, Computational Biology and Bioinformatics, advisor. “Classification of Distinct Conformers of β2-Adrenergic Receptor (β2-AR) Based on Binding Affinity of Ligands through Docking Studies” (2015-2018)

5. Canan Özgür. Master’s Thesis. Boğaziçi University, Computational Science and Engineering, co-advisor. “Allosteric Mechanism in Human β2-Adrenergic Receptor”. (2012- 2014)

4. Ayça Koroğlu. Master’s Thesis. Kadir Has University, Computational Biology and Bioinformatics, advisor. “Prediction of 3D structure of the Dimeric State of Human β2-Adrenergic Receptor”.  (2010-2016)

3. Rüya Yakar. Master’s Thesis. Kadir Has University, Computational Biology and Bioinformatics, advisor. “Pharmacophore Screening and Docking Studies to Explore Novel Inhibitors for Human β2-Adrenergic Receptor”. (2010-2013)

2. Sibel Çakan. Master’s Thesis. Kadir Has University, Computational Biology and Bioinformatics, advisor. “Exploring Intrinsic Dynamics of Human B2-Adrenergic Receptor through Coarse-Grained Molecular Dynamics”. (2010-2012)

1. Özer Özcan. Master’s Thesis. Boğaziçi University, Computational Science and Engineering, co-advisor. “Structural Dynamics of Human B2-Adrenergic Receptor”. (2010-2011)