Demet new

Doç. Dr. E. Demet Akten Akdoğan


İletişim Bilgileri:

Adres: Kadir Has Üniversitesi, Mühendislik ve Doğa Bilimleri Fakültesi, Biyoinformatik ve Genetik Bölümü, Cibali Kampüsü, D Blok, Oda No: 250
Tel: 0212 533 65 32 / ext. 1350
e-mail: demet.akten@khas.edu.tr or demet.akten@gmail.com

Eğitim :

Bosphorus Lisans (1990-1994): Boğaziçi University, Kimya Mühendisliği
Bosphorus Yüksek Lisans (1994-1996): Boğaziçi University, Kimya Mühendisliği. Tez Danışmanı: Prof. İvet Bahar
Akron        Doktora (1996-2001): Akron Üniversitesi, Polimer Bilimleri Enstitüsü (Ohio, A.B.D). Tez Danışmanı: Prof. Wayne L. Mattice

 


Akademik Tecrübe:

carnegie mellon   Doktora sonrası araştırmacı (2001-2002): Carnegie Mellon Üniversitesi, Kimya Mühendisliği. Akademik Danışman: Prof. David S. Sholl
Scripps Doktora sonrası araştırmacı (2002-2004): Novartis GNF/Scripps Araştırma Enstitüsü. Akademik Danışman: Prof. Peter Schultz
estuary Yard.Doç. (2006-2008): Haliç Üniversitesi, Moleküler Biyoloji ve Genetik 
kadir has Yard.Doç. (2008 – 2013): Kadir Has Üniversitesi, Biyoinformatik ve Genetik 
kadir has Doçent (2013 – halen): Kadir Has Üniversitesi, Biyoinformatik ve Genetik 

Ödüller:

Kadir Has Üniversitesi, Dekan Özel Ödülü Mühendislik ve Doğa Bilimleri Fakültesi (2012)


Verilen Dersler:

2018-2019 Akademik Yılı:

Fall Semester:

    • Bioinformatics I (BIO 203, Fall)
    • Bioinformatics (BIO 511, Fall)
    • Advanced Bioinformatics (BIO 611, Fall)

Spring Semester:

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

Üyelikler:

       Biophysical Society
       Protein Society


Araştırma Konuları:

       Protein Dinamiği
       Bilgisayar Destekli İlaç Tasarımı
       Biyoinformatik
       Protein Katlanma Problemi


Araştırma Projeleri:

tubitak TÜBİTAK-1001 (218M320).Identification of species-specific regions in glycolytic enzymes and their use in allosteric drug design studies”. Yürütücü. Budget: 707.756,00 TL (2019-2022)
tubitak TÜBİTAK-1001 (213M544). “Investigation of Allosteric Mechanism in Active and Inactive Transitions in Beta2-Adrenergic Receptors and Application in Drug Design Studies”. Yürütücü. Budget: $ 257,420 (2014-2016)
tubitak TÜBİTAK-1001 (113M237). “New computational approaches to unravel allosteric mechanisms and ligand binding sites”. Araştırmacı (Yürütücü: Prof. Pemra Doruker Turgut) Budget:238,000 TL (2013-2016)
tubitak TÜBİTAK-1001 (109M281), “Investigation of the Dynamic Structure of Beta-2 Adrenergic Receptor Protein and Its Importance in Computer-aided Drug Design”. Yürütücü. Budget:181,300 TL (2009-2012)
tubitak TÜBİTAK 1001 (109M213), “Hybrid algorithms and applications on protein flexibility”. Araştırmacı (Yürütücü: Prof. Pemra Doruker Turgut) Budget: 234,145 TL (2009-2012)

 Yayınlar:

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)


Kitap Bölümü:

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.


Yönetilen Tezler:

10. Serkan Çeliker, MS Thesis. Kadir Has University, Computational Biology and Bioinformatics, advisor.Identification of species-specific regions in glyceraldehyde-3-phosphate dehydrogenase  and their use in allosteric drug design studies“, (2019-present)

9. Merve Ayyıldız, MS Thesis. Kadir Has University, Computational Biology and Bioinformatics, advisor.Identification of species-specific regions in phosphofructokinase and their use in allosteric drug design studies“, (2019-present)

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”, (2018-present)

7. Nuray Söğünmez. PhD Thesis. Kadir Has University, Bioinformatics and Genetics, advisor.Allostoric Communication Pathways in Proteins(2017-present)

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)