Pemra DORUKER TURGUT

Prof.
E-mail: 

doruker@retired.bogazici.edu.tr

Address: 
Department of Chemical Engineering, Boğaziçi University, Bebek 34342, Istanbul-TURKEY
Phone: 
+90 (212) 359 7365
Web: 

http://www.prc.bogazici.edu.tr

Education: 

PhD: Chemical Engineering, Boğaziçi University, Turkey, 1995
MS: Chemical Engineering, Boğaziçi University, Turkey, 1991
BS: Chemical Engineering, Boğaziçi University, Turkey, 1987  

Honors and Awards: 

- BUVAK Award for Outstanding Success in Research (Senior), given by Bogaziçi University Foundation, 2008
- Young Scientist Award, given by TUBA (Turkish National Academy of Sciences), 2002
- Junior Science Award, given by TUBITAK (Turkish National Science and Technology Foundation), 2001
- BUVAK Award for Outstanding Success in Research (Junior), given by Bogaziçi University Foundation, 2000
- BAP Doctorate Thesis Award, Boğaziçi University, given by Bogaziçi University, 1995

Research Interests: 
  • Computational structural biology
  • Protein dynamics and interactions
  • Multi-scale modeling and simulation
Selected Papers: 
  • Uyar A., Kantarci-Carsibasi N., Haliloglu T., Doruker P. "Features of Large Hinge-Bending Conformational Transitions. Prediction of Closed Structure from Open State", Biophysical Journal, 106(12), 2656–2666, (2014)
  • Ozcan O., Uyar A., Doruker P., Akten E.D. "Effect of intracellular loop 3 on intrinsic dynamics of human beta2-adrenergic receptor", BMC Structural Biology,13(1), (16pp) (2013)
  • Kurkcuoglu Z.; Bakan A.; Kocaman D.; Bahar I.; Doruker P. "Coupling between Catalytic Loop Motions and Enzyme Global Dynamicsî PLOS Computational Biology 8, e1002705 (11pp) (2012).
  • Kurkcuoglu Z.; Ural G.; Akten E.D.; Doruker P, "Blind Dockings of Benzothiazoles to Multiple Receptor Conformations of Triosephosphate Isomerase from Trypanosoma cruzi and Humanî Molecular Informatics 30, 986-995 (2011).
  • Uyar A.; Kurkcuoglu O.; Nilsson L.; Doruker P. "The elastic network model reveals a consistent picture on the intrinsic functional dynamics of type II restriction endonucleasesî Physical Biology 8, 056001 (13pp) (2011).
  • Alakent B.; Baskan S.; Doruker P. "Effect of Ligand Binding on the Intraminimum Dynamics of Proteinsî Journal of Computational Chemistry 32, 483-496 (2011).
  • Kurkcuoglu O.; Turgut O.T.; Cansu S.; Jernigan R.L.; Doruker P. "Focused Functional Dynamics of Supramolecules by Use of a Mixed-Resolution Elastic Network Modelî Biophysical Journal 97, 1178-1187 (2009).
  • Kantarci-Carsibasi N.; Haliloglu T.; Doruker P. "Conformational Transition Pathways Explored by Monte Carlo Simulation Integrated with Collective Modes" Biophysical Journal 95, 5862-5873 (2008)
  • Cansu S.; Doruker P. "Dimerization affects collective dynamics of triosephosphate isomerase", Biochemistry, 47, 1358-1368 (2008)
  • Doruker, P; Jernigan, R. L.; Bahar, I. "Dynamics of large protein systems through hierarchical levels of coarse-grained structuresî Journal of Computational Chemistry 23, 119-127 (2002)
  • Doruker, P.; Atilgan, A. R.; Bahar, I. (2000) "Dynamics of Proteins Predicted by Molecular Dynamics Simulations and Analytical Approaches: Application to alpha-Amylase Inhibitor" Proteins, 40, 512-524.
  • Baschnagel, J.; Binder, K.; Doruker, P.; Gusev, A. A.; Hahn, O.; Kremer, K.; Mattice, W. L.; Müller-Plathe, F.; Murat, M.; Paul, W.; Santos, S.; Suter, U. W.; Tries, V. (2000) "Bridging the Gap between Atomistic and Coarse-Grained Models of Polymers: Status and Perspectives" Advances in Polymer Science 152, 41-156.
Research Laboratory: 
Polymer Research Center (PRC)