Koc University

Koc Engineering

Highlights

- Koc University will be hosting the International Workshop on Hybrid Systems: Modeling, Simulation and Optimization (May 14-16, 2008)

- Our paper on 2-stage algorithm for predicting protein secondary structures is published. (August 13, 2007)

- Metin Turkay is the recipient of IBM SUR Award. It is the first IBM SUR Award given to a researcher in Turkey. (July 18, 2007)# # # # # # #

- Metin Turkay delivers semi-plenary talk in EURO XXII Conference in Czech Republic on Operations Research in Computational Biology, Bioinformatics and Medicine (July 10, 2007).

- Our paper on QSAR Analysis of DHP Antogonosits is published. (June 9, 2007)

- Our work on drug design was featured in AKSAM daily newspaper (May 26, 2007) > #

- SystemsLab group members Fadime Uney Yuksektepe and Ali Ozturk successfully defended their PhD Proposals. (March 14, 2007)

- SystemsLab group members Fadime Uney Yuksektepe and Ali Ozturk passed the PhD Qualifying Exam. (September 14, 2006)

- Our paper on model predictive control of supply chain systems is published. (September 12, 2006)

- Metin Turkay's TÜBİTAK Young Scientist Encouragement Award is featured in Milliyet daily newspaper (August 10, 2006) >

- Metin Turkay is awarded with TUBITAK Young Scientist Encouragement Award for his contributions to mixed-integer programming (July 24, 2006)

- Our paper on collaboration for environmentally conscious energy systems is published. (Aug 10, 2006)

- Our paper on a new method for multi-class data classification is published is published. (Aug 10, 2006)

- Metin Turkay is elected as the Chair of EURO Working Group on Operational Research in Computational Biology, Bioinformatics and Medicine. (July 5, 2006)

Systems Biology Research at SystemsLab

Research Interests:
  • Optimization Models and Algorithms in Computational Biology, Bioinformatics and Medicine
  • Structure-Based Drug Discovery and Design
  • Modeling and Optimization in Biological Networks
  • Prediction of Folding Types and Secondary Structures of Proteins with Mathematical Programming Approaches
Selected Publications

  • Kaplan, U., M. Turkay, L.T. Biegler, B. Karasozen, “Modeling and Simulation of Metabolic Networks for Estimation of Biomass Accumulation Parameters”, Discrete Applied Mathematics, in print (2007).

  • Yilmaz, O., F. Uney and M. Turkay,” Prediction of Secondary Structures of Proteins Using a Two-Stage Method”, Comput. Chem. Engng., in print (2007).

  • Kahraman, P. and M. Turkay, "Classification of 1,4-Dihydropyridine Calcium Channel Antagonists using Hyper-Box Approach", Ind. Eng. Chem. Res., in print (2007).

  • Ozdemir, M.E., H. Kavakli and M. Turkay, "Structure-based design and analysis of cytochrome P450 inhibitors for the treatment of prostate cancer", Proc. BIOCOMP'06, Eds.: H.R. Arabnia and H. Valafar, 378-384 (2006).

  • Turkay, M., O. Yilmaz and F. Uney-Yuksektepe, "Prediction of Secondary Structures of Proteins Using a Two-Stage Method", Computer-Aided Chem. Eng., vol 21B: ESCAPE-16, W. Marquardt and C. Pantelides (Eds.), 1679-1685, Elsevier, Amsterdam (2006).

  • Uney, F., and M. Turkay, "A Mixed-Integer Programming Approach to Multi-Class Data Classification Problem", European Journal of Operational Research, 173(3), 910-920 (2006).

  • Gursoy, A., O. Keskin, M. Turkay, and B. Erman, “Relationships between Unfolded Configurations of Proteins and Dynamics of Folding to the Native State”, J. Polymer Sci. Part B: Polymer Phys, 44, 3667-3678 (2006).

  • Turkay, M., F. Uney and O. Yilmaz, "Prediction of Folding Type of Proteins Using Mixed-Integer Linear Programming", Computer-Aided Chem. Eng., vol 20A: ESCAPE-15, L. Puigjaner and A. Espuna (Eds.), 523-528, Elsevier, Amsterdam (2005).

  • Turkay, M., "Structural Synthesis of Small Molecule Drug Candidates", Proc. FOCAPD 2004, 395-398 (2004).

  • Keskin, O., D. Yuret, A. Gursoy, M. Turkay, and B. Erman, “Relationships between Amino Acid Sequence and Backbone Torsion Angle Preferences and Correlations in Proteins”, Proteins: Structure, Function, and Bioinformatics, 55(4), 992-998 (2004).

Other application areas:

Process Systems Engineering

Supply Chain Management and Logistics