ŞEBNEM EŞSİZ

Assistant Professor
 ŞEBNEM EŞSİZ

D BLOK 3. KAT 329

+90 (212) 533 65 32 / 1437

sebnem.gokhan@khas.edu.tr

https://sites.khas.edu.tr/bioinformatics/research/sebnem-essiz

ORCID

Education

Doctorate

UNIVERSITY OF PITTSBURGH
Biophysical Chemistry

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

2012 / Continuing Assistant Prof.
Kadir Has University

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

  • "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
  • "Investigation of Structural and Antibacterial Properties of WS2-Doped ZnO Nanoparticles",
    Beytur, Sercan ; ESSIZ, Sebnem ; Ozugur, Bengu ; , ACS Omega, (2024) Vol.9, 4037 DOI: 10.1021/acsomega.3c09041
  • "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 CO2 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 WS2-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 γ2α1β2α1β2 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
"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
Multi-scale Modeling in Chemistry CSE610 2024/25 Spring
Protein Folding MBG318 2024/25 Spring
Structural Bioinformatics MBG428 2024/25 Spring
Proteins in Motion CSE605 2024/25 Fall
Biopython MBG309*1 2024/25 Fall
Proteins in Action MBG429 2024/25 Fall

PAST GRADUATE STUDENT

STUDENTDEGREE/YEARCurrent Position
SERCAN BEYTÜRPhD-2023Bioinformatician, Paris 
BURAK SERVILIPhD-2023Core Program, KHAS
SEVILAY GÜLESENMS-2021University of Leipzig, Germany
BÜSRA SAVASMS-2021Izmir Biomedicine and Genome Center
MELIS GENCELMS-2019Université de Montréal, QC Canada
MUHAMMED AKTOLUNMS-2017Carnegie Mellon University, PA USA
AYHAN DEMIRMS-2017TUSEB, Turkiye
FATMA M AB ALNEMSIMS-2016-
MERAL AYANMS-2014Mentor Egitim Kurumlari, Turkiye