Pemra OZBEK SARICA, Ph.D.
Assistant Professor
Marmara University, Faculty of Engineering, Department of Bioengineering
Address: Marmara Üniversitesi, Mühendislik Fakültesi, Biyomuhendislik Bölümü, Göztepe Kampüsü, 34722, Kadıkoy, İstanbul, Türkiye.
E-mail: pemra.ozbek AT marmara.edu.tr
Biopolymers
Structural dynamics, modelling and simulations of biological macromolecules
Sequence-structure-dynamics-function relations in proteins
Gaussian Network Model (GNM) and applications
Protein binding site prediction
CAPRI (Critical Assessment of PRediction of Interactions)
Prediction of protein-protein interaction types
HLA molecules, autoimmune diseases
Molecular dynamics simulations
Computational docking
PhD, Mechanical Engineering August 2004- February 2008
Imperial College, London, UK
Dissertation: Rapid fracture resistance of Polyethylene: Dependence on Polymer Structure
Supervisor: Dr. Patrick S. Leevers
BSc, Chemical Engineering 1999-2004
Bogazici University, Istanbul, Turkey
Sercinoglu O., Ozbek P., Computational characterization of residue couplings and micropolymorphism-induced changes in the dynamics of two differentially disease-associated human MHC class-I alleles, Journal of Biomolecular Structure and Dynamics, 2017. doi:10.1080/07391102.2017.1295884
Sercinoglu O., Ozcan G., Kutlu Kabas Z., Ozbek P., A computational docking study on the pH dependence of peptide binding to HLA-B27 sub-types differentially associated with ankylosing spondylitis, Journal of Computer-Aided Molecular Design, 30(7), 569-581, 2016. doi:10.1007/s10822-016-9934-z
Ozbek P., Dynamic characterization of HLA-B*44 Alleles: A comparative molecular dynamics simulation study, Computational Biology and Chemistry, 62(12-16), 2016. doi:10.1016/j.compbiolchem.2016.02.019
Soner S., Ozbek P., Garzon, JI., Ben-Tal, N., Haliloglu, T., DynaFace: Discrimination between Obligatory and Non-obligatory ProteinProtein Interactions Based on the Complex’s Dynamics, PLoS Comput Biol 11(10): e1004461. 2015, doi:10.1371/ journal.pcbi.1004461
Ozbek P., Soner, S., Haliloglu, T., Hot Spots in a network of functional sites, PLOS ONE 8(9), e74320, 2013. doi: 10.1371/journal.pone.0074320
Fleishman S. et al. (Group 13: Soner,S. Ovali, S.K., Ozbek, P.,Ben Tal, N., Haliloglu, T.), Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology, Journal of Molecular Biology, 414 (2):289-302, 2011. doi: 10.1016/j.jmb.2011.09.031
Ozbek, P., Soner S., Erman B., Haliloglu, T., DNABINDPROT: fluctuation-based predictor of DNA-binding residues within a network of interacting residues, Nucleic Acids Research, Web Server issue, 38:W417-423, 2010. doi: 10.1093/nar/gkq396
Ozbek, P., Haliloglu, T., Protein Dynamics, Sigma: Journal of Engineering and Natural Sciences, 27:161-170, 2009
Ozbek, P., Argyrakis, C., Leevers, P., Fracture mechanics analysis of arc shaped specimens for pipe grade polymers, Polymer Testing, 28(3):357-361, 2009. doi:10.1016/j.polymertesting.2009.02.001
Ozbek, P., Leevers, P., Uniaxial tensile properties underlying plane stress rapid fracture resistance in polyethylene, Polymer Engineering and Science, 48(9):1855-1861, 2008. doi:10.1002/pen.21159
Ozbek, P., Leevers, P., Plane stress rapid fracture resistance of pipe grade PE: Estimation from tensile drawing data, ANTEC Conference Proceedings, 5:2880-2884, 2007
Sercinoglu, O., Ozbek, P., Quantifying Peptide Binding Affinities from Non-equilibrium Work, 62nd Biophysical Society Annual Meeting, San Francisco, USA, 17-21 February 2018.
Sercinoglu, O., Ozbek, P, A Software Tool for Parallel Computation and Characterization of Residue Interaction Energies from Molecular Dynamics Simulations, International Symposium on Chemistry via Computation Applications on Molecular Nanoscience, Istanbul,Turkey, 30 October 2017.
Bunsuz, A., Sercinoglu, O., Ozbek, P, effect of temperature on the molecular dynamics simulations of HLA-A*02 alleles, International Symposium on Chemistry via Computation Applications on Molecular Nanoscience, Istanbul,Turkey, 30 October 2017.
Bingol, EN., Sercinoglu, O., Ozbek, P, Construction of allosteric residue networks in caspase-7 using energy perturbation responses, International Symposium on Chemistry via Computation Applications on Molecular Nanoscience, Istanbul,Turkey, 30 October 2017.
Sercinoglu, O., Ozbek, P, Steered Molecular Dynamics Simulation for Efficient Ranking of Peptide - MHC Class I Binding Affinities, 5th International BAU-Drug Design Congress, İstanbul, Turkey, 19-21 October 2017, (Poster&Oral Presentation).
Bunsuz, A., Sercinoglu, O., Ozbek, P, Immunogenic Peptide - HLA-A*02:01 Complexes Studied by Comparative Molecular Dynamics Simulation, 5th International BAU-Drug Design Congress, İstanbul, Turkey, 19-21 October 2017.
Bingol, EN., Sercinoglu, O., Ozbek, P, Detection of the allosteric residue network in effector caspase molecules by energy dissipation model, 5th International BAU-Drug Design Congress, İstanbul, Turkey, 19-21 October 2017.
Bunsuz, A., Sercinoglu, O., Ozbek, P, Investigation of peptide binding affinity and thermal stability of Human Leukocyte Antigens (HLAs), 19th IUPAB and 11th EBSA Congress, Edinburgh, UK, 16-20 July 2017.
Sercinoglu, O., Ozbek, P, Allelic dependence of MHC-I stability on peptide termini contacts in MD simulations, 19th IUPAB and 11th EBSA Congress, Edinburgh, UK, 16-20 July 2017.
Bunsuz, A., Sercinoglu, O., Ozbek, P, Investigation of peptide binding affinity and complex stability of Human Leukocyte Antigens (HLAs), 4th International BAU-Drug Design Congress, İstanbul, Turkey, 12-15 October 2016.
Bingol, EN., Sercinoglu, O., Ozbek, P, Searching a communication pathway between allosteric site and binding region in effector caspase molecules, 4th International BAU-Drug Design Congress, İstanbul, Turkey, 12-15 October 2016..
Sercinoglu, O., Ozbek, P, Allelic Modulation of Global Dynamics of HLA-B*27:05 and HLA-B*27:09 Molecules, 13.Greta Pifat Mrzljak Uluslararası Biyofizik Yaz Okulu, Hırvatistan, 01-10 September 2016.
Bunsuz, A., Sercinoglu, O., Ozbek, P, HLA-B*44 Alellerinin Peptid Bağlanma Davranış Mekanizmalarının Hesaplamalı Olarak araştırılması, Biruni Üniversitesi Bilgisayar Destekli İlaç Tasarımı, İstanbul, Türkiye, 16-17 Mayıs 2016 (poster ödülü).
Bingol, E.N., Sercinoglu, O., Ozbek, P, Investigating Dynamics of HLA Molecules By Energy Dissipation, 60th Biophysical Society Meeting, Los Angeles, USA, February 27-March 2, 2016.
Kutlu Kabas, Z., Ozcan, G., Sercinoglu, O., Ozbek, P, Investigation of the Binding Behaviour of HLA-B27 Alleles at varying pH Conditions Using Computational Methods, 3rd International BAU-Drug Design Congress, Istanbul, Turkey, October 1-3, 2015.
Bunsuz A., Sercinoglu, O., Ozbek, P., Computational Study on the Binding Behaviour of HLA-B44 Alleles, 3rd International BAU-Drug Design Congress, Istanbul, Turkey, October 1-3, 2015.
Bingol, EN., Sercinoglu, O., Ozbek, P., Computational Investigation of Protein Dynamics Based On Energy Dissipation, 3rd International BAU-Drug Design Congress, Istanbul, Turkey, October 1-3, 2015.
Sercionlu, O., Ozbek, P., Structural Characterization of Peptide Binding to Class I MHC Proteins using Protein Energy Networks from Molecular Dynamics Simulations, 3rd International BAU-Drug Design Congress, Istanbul, Turkey, October 1-3, 2015.
Ozcan, G., Kutlu Kabas, Z., Sercinoglu, O., Ozbek, P., Computational Study on the Effect of pH on the Binding Behaviour of HLA-B Alleles , 10th European Biophysics Congress, Dresden, Germany, July 17-22, 2015.
Sercinoglu, O., Ozbek, P., Peptide dependent binding-stabilization effect of β2 microglobulin on HLA B27 alleles, 10th European Biophysics Congress, Dresden, Germany,July 17-22, 2015.
Ozcan, G., Kutlu Kabas, Z., Sercinoglu, O., Ozbek, P., Binding Behavior of HLA-B Alleles Related to Ankylosing Spondylitis (AS) Disease: A Comparative Study by Computational Methods, ECCB'14, the 13th European Conference on Computational Biology, Strasbourg, September 7-10, 2014.
Kutlu Kabas, Z., Ozcan, G., Sercinoglu, O., Ozbek, P., Computational Study on the Effect of pH on the Binding Behaviour of HLA-B Alleles, ECCB'14, the 13th European Conference on Computational Biology, Strasbourg, September 7-10, 2014.
Sercinoglu, O., Ozbek, P., An Investigation of the Effects of Model Simplification and Water Box Shell Size on the Molecular Dynamics Simulations of Peptide-loaded Major Histocompatibility Complex Proteins, Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery: Bridging Experiments and Computations, Istanbul, Turkey, September 10-14, 2014
Ozcan, G., Sercinoglu, O., Kutlu Kabas, Z., Ozbek, P., Comparison of the Binding Behavior of HLA-B Alleles Related to Ankylosing Spondylitis Disease by Computational Methods, Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery: Bridging Experiments and Computations, Istanbul, Turkey, September 10-14, 2014.
Sercinoglu, O., Ozcan, G., Ozbek, P., Computational Investigation of the Energy Exchange Pathways in Peptide-loaded Major Histocompatibility Complex Proteins, Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery: Bridging Experiments and Computations, Istanbul, Turkey, September 10-14, 2014.
Kaya, C., Soner, S., Ozbek, P., Haliloglu, T., The intrinsic dynamics of partner chains aid in the detection of native complexes amongst docking decoys, Seminar Presentation, CAPRI Meeting 2013, Utrecht, Holland, 2013.
Kaya, C., Onel O., Soner, S., Ozbek, P., Haliloglu, T., Unique Scoring Function for Molecular Docking of Proteins, Poster Presentation, Imperial College Hermes, Summer School on Material Simulations, London, UK, 2012.
Soner, S., Ozbek, P., Haliloglu, T. , Dynamics define protein binding, Chemical Physics Congress-IX Izmir, Turkey, 2010.
Ozbek, P., Protein-protein and protein-DNA interactions by elastic network models, Seminar Presentation, Informatics Institute, ITU, Istanbul, Turkey, 2010.
Ozbek, P., Soner, S., Chen, N., Kalman, M., Erman, B., Ben-tal, N., Haliloglu, T. , Dynamics and evolutionary conservation of inter-protein interfaces aid in the detection of native complexes amongst docking decoys, 4th CAPRI meeting, Barcelona, Spain, 2009.
Ozbek, P., Leevers, P., The origins of polyethylenes resistance to rapid, plane-stress rupture, 5th ESIS TC4 Conference on Fracture of Polymers, Composites and Adhesives, Switzerland, 2008, (Oral Presentation).
Ozbek, P., Leevers, P., Plane stress rapid fracture resistance of pipe grade PE: Estimation from tensile drawing data, ANTEC Conference Presentation, Cincinnati, OH, USA, 2007, (Oral Presentation).
Ozbek, P., New test methods for indexing toughness transitions in pipe grade polyethylene, Company Presentation, Chevron Phillips Chemical Company, Bartlesville, OK, USA, 2006, (Oral Presentation).
Biophysical Society 62th Annual Meeting, San Francisco, USA, February 17-21, 2018.
5th International BAU Drug Design Congress, Istanbul, Turkey, October 19-21, 2017.
Biophysical Society 60th Annual Meeting, Los Angeles, USA, February 27-March 3, 2016.
3rd International BAU Drug Design Congress, Istanbul, Turkey, October 1-3, 2015.
10th European Biophysics Congress, Dresden, Germany, July 18-22, 2015.
Biophysical Society Thematic Meeting: Modeling of Biomolecular Systems Interactions, Dynamics,and Allostery: Bridging Experiments and Computations, Istanbul, Turkey, September 10-14, 2014.
Joint TCBG/MMBioS Hands-on Workshop on Computational Biophysics, Pittsburgh Supercomputing Center, Pittsburgh, Pennsylvania, June 10-14, 2013.
Schrodinger Workshop, "Computational Drug Discovery", Yeditepe University, Istanbul, Turkey, April, 2012.
Three-days HADDOCK workshop in Istanbul, Bogazici University, Istanbul, Turkey, June 20-22, 2011.
PI, Moleküler Dinamik Simülasyon Bazlı Sarsım Yöntemi ile Protein İçi Sinyal İletim Mekanizmasının Karakterizasyonu, Marmara University Research Fund Project, FEN-A-100616-0273, 2016-.
PI, Computational Dynamical Characterization of Human Major Histocompatibility Complex Proteins, Marmara University Research Fund Project, FEN-C-DRP-110915-0436, 2015-.
PI, Dynamic Characterization of Protein-protein Interfaces using Gaussian Network Model, Marmara University Research Fund Project, FEN-A-120514-0155, 2014-2015.
PI, Dynamic Characterization of HLA Molecules, TUBITAK, 113M293, 2013-2015.
PI, Dynamic Characterization of Protein Binding Mechanism, Marmara University Research Fund Project, FEN-A-130612-0219, 2012-2013.
Researcher, Marmara University Research Fund Project, Structural Analysis of Von Hippel- Lindau Tumor Suppressor Protein with the Anisotropic Network Model, FEN-A-060510-0130, 2010-2013.
Post-Doctorate at Bogazici University, Polymer Research Center, 2010-2011.
Post-Doctorate at Bogazici University, Polymer Research Center, TUBITAK 2218 (Turkish National Science and Technology Foundation) fellowship, 2009-2010.
Post-Doctorate at Bogazici University, Polymer Research Center, COSBIOM (Towards Excellence in Computational Structural Biology and Biomaterials) fellowship, 2008-2009.
TUBITAK-BIDEB 2218(Turkish National Science and Technology Foundation) fellowship, 2009-2010.
Overseas Research Student Awards Scheme (ORSAS), UK, 2004-2007.
Ph.D Sponsorship, Chevron Phillips Chemical Company,2004-2007.
3rd place Award, Department of Chemical Engineering, Bogazici University, 2004.
Assistant Professor since 2011
Department of Bioengineering, Marmara University, Istanbul, Turkey
- MATH 101 Calculus I
- MATH 102 Calculus II
- PHYS 101 Physics I
- PHYS 102 Physics II
- BIOE 262 Mathematical Applications in Bioengineering Systems
- BIOE 324 Biotransport Phenomena
- BIOE 315 Biotransport Phenomena I
- BIOE 316 Biotransport Phenomena II
- BIOE 795 Special Topics in Bioengineering
- BIOE 896 Advanced Topics in Bioengineering
- BIOE 828 Advanced Molecular Dynamics of Proteins
- BIOE 767 Structural Dynamics of Proteins
M.Sc. Thesis
- Gulin OZCAN, Docking Studies in HLA Molecules, March 2015
- Zeynep KUTLU KABAS, Computational Study On The Effect of pH on the Binding Behaviour of HLA-B Alleles, July 2015
- Elif Naz BINGOL, Computational Investigation of Protein Dynamics Based on Energy Dissipation, June 2017