17. Gerek ZN, Ozkan SB, "A Flexible Docking Scheme to Explore the Binding Selectivity of PDZ Domains", Protein Science (in press 2010)

16. Glembo T, Ozkan SB, "Union of geometric simulations with molecular dynamics for protein structure prediction", Biophysical Journal (in press 2010)

15. Gerek ZN, Keskin O, Ozkan SB, "Identification of Specificity and Promiscuity of PDZ Domain Interactions through their Dynamic Behavior", Proteins (2009) 77:796-811

14. Shell MS, Ozkan SB, Voelz V, Wu AG, Dill KA, "Blind test of physics-based prediction of protein structures", Biophys. J. (2009) 96: 1

13. Dill KA, Ozkan SB, Shell MS, Weikl TR, "The protein folding problem", Ann. Rev. Biophys. Biomolec. Struct. (2008) 37: 289

12.Engen JR, Wales TE, Hochrein JM, Meyn MA III, Ozkan SB, Bahar I and Smithgall TE, "Structure and dynamic regulation of Src-family kinases", Cell Mol Life Sci. (2008) MID: 18563293

11. Ozkan SB, Wu AG, Chodera JD, Dill KA, "Protein Folding by Zipping and Assembly", Proc. Natl. Acad. Sci. USA. (2007) 104: 11987-11992

10. Dill KA, Ozkan SB, Wiekl TR, Chodera JD, Voelz VA, "The protein folding problem: when will it be solved?", Curr. Opin. Struct. Biol. (2007) 17: 342-346

9. Ghosh K, Ozkan SB, Dill KA "The Ultimate Speed Limit of Protein Folding is Conformational Searching", J. Am. Chem. Soc. (2007) 129: 11920-11927

8. Chodera, JD, Wu A, Ozkan SB and Dill KA, "Are Molecular Mechanics Forcefields Capable of Protein Structure Prediction" submitted to J. Chem. Theory Comput.

7. Ozkan SB and Meirovitch H, 'Conformation Search of Peptides and Proteins:" The Monte Carlo Minimization with Adaptive Bias Applied to Hepta-Peptide Deltorphin', Journal of Computational Chemistry (2004), 25:565-572.

6. Ozkan SB, Kirca S and Haliloglu T,"Unfolding Events of Chymotrypsin Inhibitor 2 Revealed by off-lattice Monte Carlo Simulations and their Consistency from Structure-Based Analysis of Conformations", Polymers (2004), 45 :581-595.

5. Ozkan SB and Meirovitch H, "Efficient Conformational Search Method for Peptides and Proteins: Monte Carlo Minimization with an Adaptive Bias", Journal of Physical Chemistry (2003), 107: 9128-9131.

4. Ozkan SB, Dill KA and Bahar I, "Computing the Transition State Populations in Simple Protein Models", Biopolymers (2003), 68: 35-46.

3. Ozkan SB, Dill KA and Bahar I, "Fast-Folding Protein Kinetics, Hidden Intermediates and the Sequential Stabilization Model", Protein Science (2002), 11:1958-1970

2. Ozkan SB, Bahar I and Dill KA, "Nonclassical Phi-values in Protein Folding Kinetics", Nature Structural Biology (2001) 98: 765-767

1. Ozkan B and Bahar I, " Recognition of Native Structure from a Complete Enumaration of Low Resolution Conformation with Constraints" Proteins Structure Function and Genetics (1998), 32: 211-222.