Our research is focused on theoretical models and computer simulations in biological systems. We use a broad range of methods, including lattice models, elastic-net methods, dynamics, and all-atom physics-based computer simulations to understand the principles of biomolecular interactions at different length scales. We are using these models to guide experimentalists, with whom we are interested in collaborating to develop hypothesis-driven science in computational biology.
We have several research interests: (i) To understand the principles of sequence-structure-function relationships in proteins, i.e., how the amino acid sequence encodes a protein's specific structure and function, (ii) How dynamics governs protein mechanisms, (iii) How proteins assemble into macromolecular machines, (iv) The dynamics of protein machines, and (v) The prediction of protein-protein interactions and interfaces, taking into account chain flexibility.
1. Gerek ZN, Ozkan SB, "A Flexible Docking Scheme to Explore the Binding Selectivity of PDZ Domains", Protein Science (in press 2010)
2. Glembo T, Ozkan SB, "Union of geometric simulations with molecular dynamics for protein structure prediction", Biophysical Journal (in press 2010).
3. Gerek ZN, Keskin O, Ozkan SB, "Identification of Specificity and Promiscuity of PDZ Domain Interactions through their Dynamic Behavior", Proteins (2009) 77:796-811
4. Dill KA, Ozkan SB, Shell MS, Weikl TR, "The protein folding problem", Ann. Rev. Biophys. Biomolec. Struct. (2008) 37: 289
5. Ozkan SB, Wu AG, Chodera JD, Dill KA, "Protein Folding by Zipping and Assembly", Proc. Natl. Acad. Sci. USA. (2007) 104: 11987-11992
