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  
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 .
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
Characterization and Prediction of Protein Interfaces to Infer Protein-Protein Interaction Networks, Ozlem Keskin, Nurcan Tuncbag, Attila Gursoy Current Pharmaceutical Biotechnology, 2008 , to appear
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*
O.N. Yogurtcu, B. Erdemli, R. Nussinov, M. Turkay, O. Keskin, Flexibility of interface residues, Biophysical J, 2008 (in press)
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).
Sayar M., & Holm C. Finite Size Polyelectrolyte Bundles at Thermodynamic Equilibrium, Europhys. Lett. 77, 16001 (2007).
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)
O. Keskin, R.Nussinov. "Similar Binding Sites and Different Partners: Implications to Shared Proteins in Cellular Pathways". Structure, 15(3):341-354, 2007.
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.
O. Keskin. "Binding induced experimental conformational changes of proteins correlate with their intrinsic fluctuations: A case study of antibodies" /BMC Struct. Biol. / 13, 2007.
Senturk S, Baday S, Arkun Y, Erman B. Optimum folding pathways for growing protein chains. Phys Biol. 2007 Nov 26;4(4):305-16.
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
Unal EB Kavakli IH Erman B (2006) Computational Search of the Interaction between Melanopsin and Cryptochrome2 Proteins, FEBS Journal 273: 43 Suppl.1

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

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

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

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
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.
Aytug Tuncel, I. Halil Kavakli, Ozlem Keskin: Structure Prediction of Potato Large Subunit ADP - Glucose Pyrophosphorylase. BIOCOMP 2006 : 315-321
Optimum Folding Pathways of Proteins. Their Determination and Properties. U. Guner, Y. Arkun, B. Erman. J. Chem Phys. 124, 134911
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)
Conformations of Tryptophan in Native Proteins and Comparison with Quantum Mechanical Calculations, E. Yurtsever, D. Yuret, B. Erman, Accepted, Journal of Physical Chemistry, (2006).
On the Theoretical Foundations of the Gaussian Network Model and Its Applications to Proteins, I. Bahar, C. Chennubhotla, B. Erman, Submitted, Physical Biology, (2006)
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
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.
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.
J. Blazewicz, C. Oguz , A. Swiercz and J. Weglarz, "DNA Sequencing by Hybridization via Genetic Search", Operations Research, Vol.54, pp:1185-1192, 2006.
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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