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OLD PUBLICATIONS |
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2005: |
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A. Selim Aytuna , Attila Gürsoy, Ozlem Keskin : Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces. Bioinformatics 21(12): 2850-2855 |
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T. Haliloglu, O. Keskin, B. Ma, R. Nussinov. "How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues" Biophys J . 88(3):1552-9, 2005. |
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O Keskin, R Nussinov. Favorable scaffolds: proteins with different sequence, structure and function may associate in similar ways. Protein Eng Des Sel. 18(1):11-24, 2005. |
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B Ma et al. "The contribution of the Trp/Met/Phe residues to physical interactions of p53 with cellular proteins" Phys. Biol. 2, 2005. |
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Utkan Ogmen , Ozlem Keskin , A. Selim Aytuna , Ruth Nussinov , Attila Gürsoy: PRISM: protein interactions by structural matching. Nucleic Acids Research 33 (Web-Server-Issue): 331-336 |
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2004: |
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Limbach H. J., Sayar M. , & Holm C.
Polyelectrolyte Bundles J. Phys. Condens. Matter 16, 2135-2144 (2004). |
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Ahmet Palazoglu, Attila Gürsoy, Yaman Arkun, Burak Erman: Folding Dynamics of Proteins from Denatured to Native State: Principal Component Analysis. Journal of Computational Biology 11(6): 1149-1168 |
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Relationships between amino acid sequence and backbone torsion angle preferences in proteins, O. Keskin, D. Yuret, A. Gursoy, M. Turkay, B. Erman, Proteins-Structure Function and Bioinformatics 55, 992-998 |
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Dynamics of large scale fluctuations in native proteins. Analysis based on harmonic inter-residue potentials and random external noise. A. Erkip, B. Erman, Polymer 45, 641-648 |
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Emek Demir, Ozgun Babur, Ugur Dogrusöz, Attila Gürsoy, A. Ayaz , Gürcan Gülesir, Gurkan Nisanci, Rengül Çetin-Atalay : An ontology for collaborative construction and analysis of cellular pathways. Bioinformatics 20 (3): 349-356 |
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2003: |
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A. Kocatas, Attila Gürsoy, Rengül Çetin-Atalay: Application of Data Mining Techniques to Protein-Protein Interaction Prediction. ISCIS 2003 : 316-323 |
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Worthington NE, Kavakli IH,Berrocal-Tito G, Bondo BE, and Sancar A (2003) Purification and characterization of three members of the photolyase/cryptochrome family blue-light photoreceptors from Vibrio Cholerea . Journal of Biological Chemistry 278(40):39143-54 |
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''Scaling Behavior of a Multiply Connected Fluctuating Interface in Two Dimensions'', H. Kaya, A. Kabakçioglu, and A. Erzan, Fractals 11 227-232 |
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Sayar M. , de la Cruz M. O., & Stupp S. I.
Polar Order in Nanostructured Organic Materials Europhys. Lett. 61, 334-340 (2003). |
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2002: |
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Berrin A. Yanikoglu , Burak Erman: Minimum Energy Configurations of the 2-Dimensional HP-Model of Proteins by Self-Organizing Networks. Journal of Computational Biology 9 (4): 613-620 |
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O. Keskin, Comparison of Full-atomic and Coarse-grained Models to Examine the Molecular Fluctuations of c-AMP Dependent Protein Kinase. J Biomol Struct Dyn. 20(3):333-46, 2002. |
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Emek Demir, Ozgun Babur, Ugur Dogrusöz , Attila Gürsoy, Gurkan Nisanci, Rengül Çetin-Atalay, Mehmet Ozturk: PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways. Bioinformatics 18 (7): 996-1003 (2002) |
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Keith D. Ball , Burak Erman, Ken A. Dill : The elastic net algorithm and protein structure prediction. Journal of Computational Chemistry 23 (1): 77-83 |
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