PUBLICATIONS

        2009

  • G. Kar, A. Gursoy, O. Keskin. Human cancer protein-protein interaction network: a structural perspective, PLoS Computational Biology, Forthcoming
  • I. Baris, A. Tuncel, N. Ozber, O. Keskin, H. Kavakli. Free energy decomposition of the potato ADPglucose Pyrophosphorylase identifies critical residues in the heterotetramer interface, PLoS Computational Biology, Forthcoming
  • Z.N. Gerek, O. Keskin, B. Ozkan. Identification of Specificity and Promiscuity of PDZ Domain Interactions through their Dynamic Behavior, Proteins. In press
  • N. Tuncbag, G Kar, O. Keskin, A. Gursoy, R. Nussinov. Inferring Time Dimensionality in Protein - Protein Interaction Networks by Integrating Structures: The p53 Example, Mol Biosys. In press
  • N. Tuncbag, A. Gursoy, O. Keskin. Identification of Computational Hot Spots in Protein Interfaces: Combining Solvent Accessibility and Inter-Residue Potentials Improves the Accuracy. Bioinformatics Forthcoming
  • N. Tuncbag, G Kar, O. Keskin, A. Gursoy, R. Nussinov. A Survey of available tools and web servers for analysis of protein-protein interactions and interfaces, Briefings in Bioinfomatics, Forthcoming

        2008

  • A. Gursoy, O. Keskin. R. Nussinov. Topological Properties of Protein Interaction Networks from a Structural Perspective, Biochemical Society Transactions, 2008 Dec;36(Pt 6):1398-403.
  • S. Ahmad, O. Keskin, A. Sarai, R. Nussinov. Protein-DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins. Nucleic Acids Res. Nucleic Acids Res. 36(18):5922-32, 2008.
  • A. Tuncel, I.H. Kavakli, O. Keskin. Insights into Subunit Interactions in the Heterotetrameric Structure of Potato ADP-glucose Pyrophosphorylase. Biophysical J, 95(8):3628-39, 2008.
  • N. Tuncbag, E. Guney, R. Nussinov , A. Gursoy, O. Keskin. Architectures and Functional Coverage of Protein-Protein Interfaces, J. Mol. Biol. 381(3):785-802, 2008.
  • O. Keskin, N. Tuncbag, A. Gursoy,  Characterization and Prediction of Protein Interfaces to Infer Protein-Protein Interaction Networks, Curr Pharmacet Biotech, 9(2):67-76, 2008.
  • O. Keskin, A. Gursoy, B. Ma, R. Nussinov, What is the preferred ways for proteins to interact, Chemical Rev., 108(4):1225-1244, 2008.
  • O.N. Yogurtcu, B. Erdemli, R. Nussinov, M. Turkay, O. Keskin, Restricted mobility of conserved residues in protein-protein interfaces in molecular simulations, Biophysical J, 94(9):3475-85, 2008.
  • E. Guney, N. Tuncbag, O. Keskin, A. Gursoy. HotSprint: database of computational hot spots in protein interfaces. Nucleic Acids Res. 2008 Jan;36(Database issue):D662-6.

        2007

  • O. Keskin. Binding induced experimental conformational changes of proteins correlate with their intrinsic fluctuations: A case study of antibodies. BMC Struct. Biol.  7: 31, 2007.
  • O. Keskin, A. Gursoy, B. Ma, R.Nussinov. Towards Drugs Targetýng Multýple Proteýns In A Systems Biology Approach. Curr. Top. Med. Chem,  7 (10): 943-951, 2007.
  • O. Keskin, R.Nussinov. Similar Binding Sites and Different Partners: Implications to Shared Proteins in Cellular Pathways. Structure, 15 (3):341-354, 2007.

        2006

  • A. Gursoy, O. Keskin, M. Turkay, B. Erman. Relationships between Unfolded Configurations of Proteins and Dynamics of Folding to the Native State. J. Polym. Sci., Part B: Polym. Phys. 44 (24): 3667-3678, 2006.

        2005

  • U. Ogmen, O. Keskin, A.S. Aytuna, R. Nussinov, A. Gursoy.  PRISM: protein interactions by structural matching. Nucleic Acids Res. 33 (Web Server issue):W331-6, 2005.
  • AS Aytuna, A Gursoy, O Keskin. Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces Bioinformatics. 21(12):2850-5. 2005.
  • O Keskin  et al Protein-protein interactions: organization, cooperativity and mapping in a bottom-up systems biology approach,  Phys. Biol. 2  S24-S35, 2005.
  • B Ma  et al. The contribution of the Trp/Met/Phe residues to physical interactions of p53 with cellular proteins Phys. Biol. 2, 2005.
  • 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.
  • O. Keskin, B. Ma, R. Nussinov, Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues. J Mol Biol. 345(5):1281-94, 2005.
  • 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.
  • M. C. Demirel, O. Keskin. Protein Interactions and Fluctuations in a Proteomic Network using an Elastic Network Model. J Biomol Struct Dyn. 2005 Feb;22(4):381-6. Review.

        2004

  • X. Li, O.Keskin, B. Ma, R. Nussinov, J. Liang.  Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking.  J Mol Biol,  2004 Nov 26;344(3):781-95.
  • O. Keskin, C.J. Tsai, H. Wolfson, R. Nussinov, A new, structurally non-redundant, diverse dataset of protein-protein interfaces and its implications. Protein Sci. 13(4):1043-1055, 2004.(pdf)
  • Y Pan, B Ma, O Keskin, R Nussinov. Characterization of the conformational state and flexibility of HIV-1 glycoprotein gp120 core domain. J Biol Chem. 279(29):30523-30, 2004.
  • O. Keskin, D. Yuret, A. Gursoy, M. Turkay, B. Erman. Relationships between amino acid sequence and backbone torsion angle preferences. Proteins. 55(4): 992-998, 2004.

        2002

  • 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.
  • O. Keskin, X. Ji, J. Blaszcyk, D.G. Covell. Molecular motions and conformational changes of HPPK. Protein, 49(2):191-205, 2002.
  • O. Keskin, S. Durell, I. Bahar, R.L. Jernigan, and D.G. Covell. Relating global motions of tubulin to its function. Biophys J. 83(2):663-80, 2002.
  • O. Keskin, I. Bahar, D. Flatow, D.G. Covell, and R.L. Jernigan. Dynamics of GroEL/GroES complex. Biochemistry, 41(2):491-501, 2002.

        2001

  • A.R. Atilgan, S.R. Durell, R.L. Jernigan, M.C. Demirel, O. Keskin and I. Bahar, Anisotropy of Fluctuation Dynamics of Proteins with an elastic network model. Biophysical Journal. Vol 80, pg. 505-515, 2001.

        2000

  • O. Keskin, R. L. Jernigan & I. Bahar, Proteins with similar architecture exhibit common large-scale dynamic behavior. Biophysical Journal, Vol. 78, pg. 2093-2106, 2000.
  • O. Keskin, I. Bahar, R.L. Jernigan, T.G. Myers, J.A. Beutler, R.H. Shoemaker, E.A. Sausville and D.G. Covell, Characterization of Anticancer Agents by their Growth-Inhibitory Activity and Relationships to Mechanism of Action and Structure, Anti-Cancer Drug Design, Vol 15, pg. 79-98, 2000.
  • G. Duman, O. Keskin,I. Bahar, J. R. Robinson, Stabilization of Molten Globular State of Hen Egg Lysozyme with Solutions Containing Polyvinyl Pyrrolidone. J Controlled Release, Vol 64 (1-3), pg. 331-333, 2000. 

        1998

  • O. Keskin, I. Bahar, A. Ya. Badretdinov, O. B. Ptitsyn, & R. L. Jernigan. Solvent-mediated inter-residue potentials at protein-protein interfaces exhibit close similarity to those in protein monomers. Protein Science, Vol 7, Number 12- pg. 2578-2586, 1998.
  • O. Keskin, I. Bahar, Packing of sidechains in low resolution models for proteins. Folding & Design, Vol 3, pg. 469-479, 1998.
  • S. Sunol, O. Keskin, O. Guney, A. Sunol, Supercritical Fluid Aided Preparation of aerogels and their Characterization. ACS Symposium Series, Chap.17, Vol. 608, pg. 258-268, San Francisco, 1995.

 BOOK CHAPTERS

CONFERENCE PUBLICATIONS

O. Keskin, T. Haliloglu, B. Ma, R. Nussinov. “Protein-protein interactions: Structurally conserved residues at protein-protein interfaces“,Biophysical Journal, Vol. 86 (1): 267A-267A, 2004.

X. Li, O. Keskin, B. Ma, R. Nussinov. “Interfacial pockets, structurally conserved residues, and energetic hot spots in protein-protein interactions“, Biophysical Journal, Vol. 86 (1): 301A-301A, 2004.

O.Keskin,  CJ Tsai, H. Wolfson, R. Nussinov. “A new dataset of non-redundant protein/protein interfaces”, Biophysical Journal, Vol. 84, pg. 42a, 2003.

O. Keskin, X. Ji, J. Blaszcyk, D.G. Covell. “Molecular motions and conformational changes of HPPK”, Biophysical Journal, Vol. 82, pg. 319a, 2002.

O. Keskin, I. Bahar, D.G. Covell, A.R. Atilgan, S. Durell, R.L. Jernigan. “Large functional motions of proteins” Biophysical Journal. Vol 80, pg. 173A-173A, 2001.

O. Keskin, I. Bahar, R.L. Jernigan, D.G. Covell, “Characterization of Anticancer Agents and their Growth Inhibitory Potency: Relationships between Potency and Chemical Substructure”, Biophysical Journal, Vol 76, pg. A384-A384, 1999.

S.G. Sunol, Keskin, O., Guney, O., Sunol A.K., Supercritical fluid aided preparation of aerogels and their characterization, Proceedings of the 3rd International Symposium on Supercritical Fluids, Tome 3, Reactions, Material Science, Chromatography and Analytical SFE, I.N.P.L. A.R., Nancy, France (1994) p. 387-392.

 

POSTER PRESENTATIONS/TALKS AT CONFERENCES

O. Keskin, D. Yuret, A. Gursoy, M. Turkay, B. Erman. “Determination of protein folding trajectories by monte carlo simulation based on go-type potentials”. AICHE Annual Meeting, November 2003, San Francisco, USA.

 

O.Keskin, T. Haliloglu, B. Ma, R. Nussinov. “A new dataset of non-redundant protein/protein interfaces”, 5th ICSMB, September 2003, Vienna, Austria.

 

O. Keskin, “Tubulin dynamics”, Protein Structure Prediction Workshop, November, 2002, Antalya, Turkey

 

O. Keskin, C.J. Tsai, H. Wolfson, R. Nussinov.  “A New Dataset of Non-Redundant Protein/Protein Interfaces”, 47th Annual Meeting of Biophysical Society Meeting, San Antonio, Texas, USA, 1-5 March 2003.

 

O. Keskin. “Assessing Global Molecular Motions Of Large Mole Cules: Relating Tubulin Flexibility To Its Functions” Protein Structure Prediction Workshop - November 1-3, 2002, Antalya, Turkey.

 

Yilmaz, O., M. Türkay, S. Savas, E. Kaya. S.B. Sonuc, M. E. Coskun, and O. Keskin. A Novel Branch and Bound Algorithm for Determining Secondary Structures of Proteins, INFORMS Annual Meeting, San Jose, CA, November, 2002.

 

O. Keskin, R. Munshi and I. Bahar. Genes in cocaine addiction, RECOMB2002, 17-21 April, 2002,Washington DC, USA, Published in the Proceedings of the Conference. 2002.

 

O. Keskin, X. Ji, J. Blaszcyk, and D.G. Covell. “Molecular motions and conformational changes of HPPK”, 46th Annual Meeting of Biophysical Society Meeting, San Francisco, CA, USA. 23-27 Feb. 2002.

 

P. Doruker, O. Keskin, R. L. Jernigan, I. Bahar. “Calculation of protein motions with extremely coarse grained models”.  4th European Symposium of the Protein Society, 18-22 April 2001, Paris, France. Protein Sci. Vol. Pp. 2001.

 

O. Keskin, I. Bahar, D.G. Covell, A.R. Atilgan, S. Durell, R.L. Jernigan. “Large functional motions of proteins”. Biophysical Society Meeting, Boston, MA, USA. 17-21 Feb. 2001.

 

O. Keskin, S. Durell, R.L. Jernigan, and D. G. Covell, “Relating Global Molecular Motions of Microtubule to its Function”, 5-9 August, 2000, 14th Annual Symposium of the Protein Society, San Diego, CA, USA. Protein Sci. Vol. 9(1), pp.122, 2000.

 

O. Keskin, S. Durell, R. L. Jernigan, and D. G. Covell, “Global Motions: Relating of Tubulin”, 13-15 June 2000, Computational Biophysics, Nice, France.

 

O. Keskin, S. Durell, R. L. Jernigan, and D. G.  Covell, “Assessing Global Molecular Motions: Relating Tubulin Flexibility to Function”, 18-21 March 2000, 5th Johns Hopkins Protein Folding Meeting, VA, USA.

 

O. Keskin, I. Bahar, R. L. Jernigan, D.G. Covell, “Characterization of Anticancer Agents and their Growth Inhibitory Potency: Relationships between Potency and Chemical Substructure”, 24-28 July.1999, 13th Annual Symposium of the Protein Society, Boston, Massachusetts, USA.

 

O. Keskin, R. L. Jernigan & I. Bahar, “Proteins with similar architecture exhibit common large-scale dynamic behavior. Specificity resides in local differences”, 24-28 July.1999, 13th Annual Symposium of the Protein Society, Boston, Massachusetts, USA.

 

O. Keskin, I. Bahar, R. L. Jernigan, D.G. Covell, “Characterization of Anticancer Agents and their Growth Inhibitory Potency: Relationships between Potency and Chemical Substructure”, 13-17 Feb.1999, Biophysical Society Meeting, Baltimore, USA.

 

G. Duman, O. Keskin, I. Bahar, J. R. Robinson, “Stabilization of Hen Egg Lysozyme    with Solutions Containing Polyvinyl Pyrrolidone” presented as poster in the Fifth European Symposium on Controlled Drug Delivery, 1-3 April 1998, Noordwijk aan Zee, The Netherlands.

 

O. Keskin, B. Ozkan, I. Bahar, “Side Chain Packing in Protein Structures”, presented as poster in 8th European Congress on Biotechnology, 17-21 August 1997, Budapest, Hungary. Published in the Proceedings of the Symposium.

 

B. Ozkan, O. Keskin, I. Bahar, “Identification of Native Conformations of Proteins Using a Low Resolution Model”, presented as poster in 8th European Congress on Biotechnology, 17-21 August 1997, Budapest, Hungary. Published in the Proceedings of the Symposium.

 

O. Keskin, I. Bahar, “Side Chain Packing in Protein Structures in Low Resolution Model”, 4th Statistical Physics Days, June 17-18,1997, Istanbul Technical Univesity, Istanbul.

 

S. Sunol, O. Keskin, O. Guney, A. Sunol, “Supercritical Fluid Aided Preparation of Aerogels and their Characterization” presented as poster in 3rd International Symposium on Supercritical Fluids, 17-19 October, 1994, Strasbourg, France. Published in the Proceedings of the Symposium.

 

S. Sunol, O. Keskin, O. Guney, A. Sunol, “Supercritical Fluid Aided Preparation of Aerogels and their Characterization” AICHE Annual Meeting, San Francisco, CA, 13-18 November, 1994. Published in the Proceedings of the Symposium.