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PUBLICATIONS |
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2008: |
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Emre Guney, Nuran Tuncbag, Ozlem Keskin, Attila Gursoy,
HotSprint: database of computational hot spots in protein interfaces,
Nucleic Acids Res. 2008 Jan;36 (Database issue) D662-6. 2007 |
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Subasi , E ., Basdogan , C., 2008, "A New Haptic Interaction and Visualization Approach for Rigid Molecular Docking in Virtual Environments", Presence: Teleoperators and Virtual Environments , MIT Press , Vol . 17, No.1, pp . 73-90 . |
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Architectures and Functional Coverage of Protein-Protein Interfaces Nurcan Tuncbag; Attila Gursoy; Emre Guney; Ruth Nussinov; Ozlem
Keskin
Architectures and Functional Coverage of Protein-Protein Interfaces,
JMB, 2008, to appear |
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Characterization and Prediction of Protein Interfaces to Infer
Protein-Protein Interaction Networks,
Ozlem Keskin, Nurcan Tuncbag, Attila Gursoy
Current Pharmaceutical Biotechnology, 2008 , to appear |
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Ozlem Keskin, Attila Gursoy,Buyong Ma,Ruth Nussinov, Principles of
Protein-Protein Interactions: What are the Preferred Ways For Proteins
To Interact? Chemical Reviews, 2008, in press* |
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O.N. Yogurtcu, B. Erdemli, R. Nussinov, M. Turkay, O. Keskin,
Flexibility of interface residues, Biophysical J, 2008 (in press) |
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2007: |
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Hess B., Sayar M., & Holm C. Stability of Hydrophobically Modified Poly(p-phenylene)sulfonate Bundles as Observed by Molecular Dynamics Simulation,
Macromolecules. 40, 1703 (2007). |
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Sayar M., & Holm C. Finite Size Polyelectrolyte Bundles at Thermodynamic Equilibrium,
Europhys. Lett. 77, 16001 (2007). |
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Emanuel M., Mohrbach H., Sayar M., Schiessel H, and Kulic I.M. Buckling of stiff polymers: Influence of thermal fluctuations Phys. Rev. E 76, 061907 (2007) |
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O. Keskin, R.Nussinov. "Similar Binding Sites and Different Partners:
Implications to Shared Proteins in Cellular Pathways". Structure,
15(3):341-354, 2007. |
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O. Keskin, A. Gursoy, B. Ma, R.Nussinov. "Towards Drugs Targeting
Multiple Proteins In A Systems Biology Approach" Curr. Top. Med. Chem,
in press, 2007. |
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O. Keskin. "Binding induced experimental conformational changes of
proteins correlate with their intrinsic fluctuations: A case study of
antibodies" /BMC Struct. Biol. / 13, 2007. |
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Senturk S, Baday S, Arkun Y, Erman B.
Optimum folding pathways for growing protein chains. Phys Biol. 2007 Nov 26;4(4):305-16. |
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Keskin O, Gursoy A, Ma B, Nussinov R. Towards drugs targeting multiple
proteins in a systems biology approach, Current Topics in Medicinal
Chemistry 7 (10): 943-951 2007 |
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Unal EB Kavakli IH Erman B (2006) Computational Search of the Interaction between Melanopsin and Cryptochrome2 Proteins, FEBS Journal 273: 43 Suppl.1 |
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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 |
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Kahraman, P. and M. Turkay, "Classification of 1,4-Dihydropyridine Calcium Channel Antagonists using Hyper-Box Approach", Ind. Eng. Chem. Res., in print |
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L. Ormeci, A. Gursoy, G. Tunca, B. Erman, ''Computational Basis of Knowledge-Based Conformational Probabilities Derived from Local and
Long-Range Interactions in Proteins", Proteins: Structure, Function, and
Bioinformatics, 66(1):29-40 , 2007. |
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Yilmaz, O., F. Uney and M. Turkay, "Prediction of Secondary Structures of Proteins Using a Two-Stage Method”, Comput. Chem. Engng., in print |
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2006: |
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A. Gursoy, O. Keskin, M. Turkay, B. Erman, ''Relationships between
Unfolded Configurations of Proteins and Dynamics of Folding to the
Native State", Journal of Polymer Science Part B: Polymer Physics, Vol.
44, 3667-3678, 2006 |
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Erman B.
The gaussian network model: precise prediction of residue fluctuations
and application to binding problems. Biophys J. 2006 Nov 15;91(10):3589-99. 2006 Aug 25. |
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Aytug Tuncel, I. Halil Kavakli, Ozlem Keskin: Structure Prediction of Potato Large Subunit ADP - Glucose Pyrophosphorylase. BIOCOMP 2006 : 315-321 |
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Optimum Folding Pathways of Proteins. Their Determination and Properties. U. Guner, Y. Arkun, B. Erman. J. Chem Phys. 124, 134911 |
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Aggregation of Fillers Blended into Random Elastomeric Networks: Theory and Comparison with Experiments, M. Demir, Y. Z. Menceloglu, B. Erman, Macromol.Chem.Phys, 207,1515–1524 (2006) |
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Conformations of Tryptophan in Native Proteins and Comparison with Quantum Mechanical Calculations, E. Yurtsever, D. Yuret, B. Erman, Accepted, Journal of Physical Chemistry, (2006). |
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On the Theoretical Foundations of the Gaussian Network Model and Its Applications to Proteins, I. Bahar, C. Chennubhotla, B. Erman, Submitted, Physical Biology, (2006) |
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M. Emre Ozdemir, I. Halil Kavakli, Metin Türkay : Structure-Based Design and Analysis of Cytochrome P450 Inhibitors for the Treatment of Prostate Cancer. BIOCOMP 2006: 378-384 |
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J. Blazewicz, B. Dziurdza, W. T. Markiewicz and C. Oguz, "The Parallel Genetic Algorithm for Designing DNA Randomizations in a Combinatorial Protein Experiment", Lecture Notes in Computer Science, Vol.3911, pp:1097-1105, 2006. |
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J. Blazewicz, F. Glover, M. Kasprzak, W. T. Markiewicz, C. Oguz, D. Rebholz-Schuhmann and A. Swiercz, "Dealing with Repetitions in Sequencing by Hybridization"', Computational Biology and Chemistry, Vol.30, pp:313-394, 2006. |
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J. Blazewicz, C. Oguz , A. Swiercz and J. Weglarz, "DNA Sequencing by Hybridization via Genetic Search", Operations Research, Vol.54, pp:1185-1192, 2006. |
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Osman N. Yogurtçu, Engin Erzin, Attila Gürsoy: Extracting Gene Regulation Information from Microarray Time-Series Data Using Hidden Markov Models. ISCIS 2006: 144-153 |
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