Associate Professor
ŞEBNEM EŞSİZ
Head of the Department of Molecular Biology and Genetics
D BLOK 3. KAT 329
+90 (212) 533 65 32 / 1437
Education
Doctorate
UNIVERSITY OF PITTSBURGH
Biophysical Chemistry (Integrated PhD)
Bachelor's Degree
KOC UNIVERSITY
Chemistry
Research Areas
- Hesaplamalı Yapısal Biyoloji ve Biyoinformatik
- NMDA ve GABA Sinir Hücresi Reseptörleri ve Membran Proteinleri
- Hızlandırılmış Moleküler Dinamik Simulasyonları
- Genetik algoritma ile protein homoloji modellemesi
Work Experience
2024 /
Continuing
Kadir Has University
Associate Prof. Dr.
2023 /
2024
Visiting Faculty Scholar
Biotechnology Dept.,
Lawrence Livermore National Lab, CA USA
2012 /
2024
Kadir Has University
Assistant Prof. Dr.
2011 /
2012
Post-Doctoral Scholar
Biotechnology Dept.,
Lawrence Livermore National Lab, CA USA
2009 /
2010
Post Doctoral Researcher
Department of Bioengineering,
Univ. of California at San Francisco
Publications
-
"Free Energy and Flexibility Analysis of Autoinhibited Human BRAF",
Tempkin, Jeremy O.B.; Aydin, Fikret; Essiz, Sebnem; Yang, Yue; Carpenter, Timothy S.; Durrant, David E.; Morrison, Deborah K.; Ingólfsson, Helgi I.; Streitz, Frederick H.; Nissely, Dwight V.; Lightstone, Felice C.; Zhang, Xiaohua; , Journal of Chemical Information and Modeling, (2026) Vol.66, No.9, 5372-5381 DOI: 10.1021/acs.jcim.5c03126 -
"Dynamics of C-terminal tail of human STING structure, active and inactive conformations",
Poyraz, Yagmur; Kavalcı, Zeynep; Ozcicek, Ece ; ESSIZ, Sebnem; , The European Chemistry and Biotechnology Journal, (2026) Vol.5, 1-13 DOI: 10.62063/ecb-56 -
"Engineering of Geobacillus kaustophilus lipase for enhanced catalytic efficiency and methanol tolerance in biodiesel production from sunflower oil",
Tülek, Ahmet; Poyraz, Yağmur; Şükür, Gözde; Paçal, Nurettin; Özdemir, F. İnci; Yildirim, Deniz; Eşsiz, Şebnem; , International Journal of Biological Macromolecules, (2025) Vol.331, DOI: 10.1016/j.ijbiomac.2025.148467 -
"Protein Homology Modeling in the Low Sequence Similarity Regime",
Eşsiz, Şebnem; , Black Sea Journal of Engineering and Science, (2024) Vol.7, No.2, DOI: https://doi.org/10.34248/bsengineering.1402011 -
"Synthesis of New Imidazo[1,2-a]pyridine Triazole Hybrid Molecules as Potential Apoptotic Antitumor Agents",
Albayrak Halac, Fatma; Essiz, Sebnem; Servili, Burak; Altundas, Ramazan; Onur Sucu, Bilgesu; Kulu, Irem; , ChemistrySelect, (2024) Vol.9, No.8, DOI: 10.1002/slct.202304911 -
"Newly synthesized 6-substituted piperazine/phenyl-9-cyclopentyl containing purine nucleobase analogs act as potent anticancer agents and induce apoptosis via inhibiting Src in hepatocellular carcinoma cells",
Bilget Guven, Ebru; Durmaz Sahin, Irem; Altiparmak, Duygu; Servili, Burak; Essiz, Sebnem; Cetin-Atalay, Rengul; Tuncbilek, Meral; , RSC Medicinal Chemistry, (2023) DOI: 10.1039/d3md00440f -
"Sustainable production of formic acid from CO
2 by a novel immobilized mutant formate dehydrogenase",
Tülek, Ahmet; Günay, Elif; Servili, Burak; Essiz, Sebnem; Binay, Barış; Yildirim, Deniz; , Separation and Purification Technology, (2023) Vol.309, DOI: 10.1016/j.seppur.2022.123090 -
"Investigation of Structural and Antibacterial Properties of WS
2 -Doped ZnO Nanoparticles",
Beytür, Sercan; Essiz, Sebnem; Özuğur Uysal, Bengü; , ACS Omega, (2023) DOI: 10.1021/acsomega.3c09041 -
"Modelling of C-terminal tail of human STING and its interaction with tank-binding kinase 1",
Ata Ouda Al-Masri, Rahaf; Audu-Bida, Hajara; Eşsiz, Şebnem; , Turkish Journal of Biology, (2022) Vol.46, No.1, 69-81 DOI: 10.3906/biy-2108-90 -
"Correlated conformational dynamics of the human GluN1-GluN2A type N-methyl-D-aspartate (NMDA) receptor",
Essiz, Sebnem; Gencel, Melis; Aktolun, Muhammed; Demir, Ayhan; Carpenter, Timothy S.; Servili, Burak; , Journal of Molecular Modeling, (2021) Vol.27, No.6, DOI: 10.1007/s00894-021-04755-8 -
"Corrigendum to “Discovery of new azoles with potent activity against Candida spp. and Candida albicans biofilms through virtual screening” [Eur. J. Med. Chem. 179 (2019) 634–648](S0223523419306105)(10.1016/j.ejmech.2019.06.083)",
Sari, Suat; Kart, Didem; Öztürk, Naile; Kaynak, F. Betül; Gencel, Melis; Taşkor, Gülce; Karakurt, Arzu; Saraç, Selma; Eşsiz, Şebnem; Dalkara, Sevim; , European Journal of Medicinal Chemistry, (2020) Vol.190, DOI: 10.1016/j.ejmech.2020.112130 -
"Synthesis, biological evaluation and molecular docking studies of bis-chalcone derivatives as xanthine oxidase inhibitors and anticancer agents",
Burmaoglu, Serdar; Ozcan, S.; Balcioglu, S.; Gencel, M.; Noma, Samir Abbas Ali; Essiz, Sebnem; Ates, Burhan; Algul, Oztekin; , Bioorganic Chemistry, (2019) Vol.91, DOI: 10.1016/j.bioorg.2019.103149 -
"Discovery of new azoles with potent activity against Candida spp. and Candida albicans biofilms through virtual screening",
Sari, Suat; Kart, D.; Öztürk, N.; Kaynak, F. Betül; Gencel, M.; Taşkor, Gülce; Karakurt, Arzu; Saraç, S.; Eşsiz, Şebnem; Dalkara, S.; , European Journal of Medicinal Chemistry, (2019) Vol.179, 634-648 DOI: 10.1016/j.ejmech.2019.06.083 -
"Antifungal screening and in silico mechanistic studies of an in-house azole library",
Sari, Suat; Kart, Didem; Sabuncuoğlu, Suna; Doğan, İnci Selin; Özdemir, Zeynep; Bozbey, İrem; Gencel, Melis; Eşsiz, Şebnem; Reynisson, Jóhannes; Karakurt, Arzu; Saraç, Selma; Dalkara, Sevim; , Chemical Biology and Drug Design, (2019) Vol.94, No.5, 1944-1955 DOI: 10.1111/cbdd.13587 -
"The neural γ
2 α1 β2 α1 β2 gamma amino butyric acid ion channel receptor: structural analysis of the effects of the ivermectin molecule and disulfide bridges",
Ayan, Meral; Essiz, Sebnem; , Journal of Molecular Modeling, (2018) Vol.24, No.8, DOI: 10.1007/s00894-018-3739-z -
"New azole derivatives showing antimicrobial effects and their mechanism of antifungal activity by molecular modeling studies",
Doğan, İnci Selin; Saraç, Selma; Sari, Suat; Kart, Didem; Eşsiz Gökhan, Şebnem; Vural, İmran; Dalkara, Sevim; , European Journal of Medicinal Chemistry, (2017) Vol.130, 124-138 DOI: 10.1016/j.ejmech.2017.02.035 -
"A wrench in the works of human acetylcholinesterase: Soman induced conformational changes revealed by molecular dynamics simulations",
Bennion, Brian J.; Essiz, Sebnem G.; Lau, Edmond Y.; Fattebert, Jean Luc; Emigh, Aiyana; Lightstone, Felice C.; , PLoS ONE, (2015) Vol.10, No.4, DOI: 10.1371/journal.pone.0121092 -
"Computational analysis of a Zn-bound tris(imidazolyl) calix[6]arene aqua complex: Toward incorporating second-coordination sphere effects into carbonic anhydrase biomimetics",
Koziol, Lucas; Essiz, Sebnem G.; Wong, Sergio E.; Lau, Edmond Y.; Valdez, Carlos A.; Satcher, Joe H.; Aines, Roger D.; Lightstone, Felice C.; , Journal of Chemical Theory and Computation, (2013) Vol.9, No.3, 1320-1327 DOI: 10.1021/ct3008793 -
"Dynamic linear response theory for conformational relaxation of proteins",
Essiz, Sebnem G.; Coalson, Rob D.; , Journal of Physical Chemistry B, (2009) Vol.113, No.31, 10859-10869 DOI: 10.1021/jp900745u -
"Langevin dynamics of molecules with internal rigid fragments in the harmonic regime",
Essiz, Sebnem G.; Coalson, Rob D.; , Journal of Chemical Physics, (2007) Vol.127, No.10, DOI: 10.1063/1.2756044 -
"A rigid-body Newtonian propagation scheme based on instantaneous decomposition into rotation and translation blocks",
Essiz, Sebnem; Coalson, Rob D.; , Journal of Chemical Physics, (2006) Vol.124, No.14, DOI: 10.1063/1.2158996 -
"A coarse graining approach in molecular simulations: Fuzzy potentials",
Eşsiz, Şebnem; Yurtsever, Ersin; , ARI Bulletin of the Istanbul Technical University, (2003) Vol.53, No.1, 25-28 -
"A coarse graining approach in molecular simulations: Fuzzy potentials",
Eşsiz, Şebnem; Yurtsever, Ersin; , Bulletin of the Technical University of Istanbul, (2003) Vol.53, No.1, 25-28
Projects
| Project Name | Role in the Project | Project Type | Fund Establishment | Start Date | End Date |
|---|---|---|---|---|---|
| "Çok ölçekli simülasyon ve modelleme ile insan BRAF kompleks yapısı, dimer olusumu ve RAS/RAF/MEK sinyal yolagındaki etkilesimlerinin incelenmesi" | Yürütücü | Ulusal Proje | TÜBİTAK ARDEB |
01.10.2025 |
01.10.2027 |
| "NMDA Tipi Glutamat Reseptörlerinin Çalışma Mekanizması ve Açık İyon Kanalı İnhibitörleri ile Etkileşimleri / Gating Mechanism of NMDA type Ionotropic Glutamate Receptor Model and Open Channel" | Yürütücü | Ulusal Proje | TÜBİTAK ARDEB |
01.04.2014 |
01.11.2018 |
Courses Offered
| Course Name | Course Code | Period |
|---|---|---|
| Structural Bioinformatics | MBG428 | 2025/26 Fall |
| Introduction to Programming via Python | MBG309*2 | 2025/26 Fall |
| Graduate Project I | MBG411*1 | 2025/26 Fall |
| Biopython | MBG309*1 | 2025/26 Fall |
PAST GRADUATE STUDENT
| STUDENT | DEGREE/YEAR | Current Position |
| SERCAN BEYTÜR | PhD-2023 | Bioinformatician, Paris |
| BURAK SERVILI | PhD-2023 | Core Program, KHAS |
| SEVILAY GÜLESEN | MS-2021 | University of Leipzig, Germany |
| BÜSRA SAVAS | MS-2021 | Izmir Biomedicine and Genome Center |
| MELIS GENCEL | MS-2019 | Université de Montréal, QC Canada |
| MUHAMMED AKTOLUN | MS-2017 | Carnegie Mellon University, PA USA |
| AYHAN DEMIR | MS-2017 | TUSEB, Turkiye |
| FATMA M AB ALNEMSI | MS-2016 | - |
| MERAL AYAN | MS-2014 | Mentor Egitim Kurumlari, Turkiye |