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  1. 1.   Normal Mode Analysis of KRas4B Reveals Partner Specific Dynamics
  2. Eren, Meryem; Tuncbag, Nurcan; Jang,Hyunbum; Nussinov,Ruth; Gursoy, Attila; Keskin, Ozlem
  3. The journal of physical chemistry. B. 2021, May 27; 125(20): 5210-5221.
  1. 2.   Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM
  2. Tuncbag, N.; Gursoy, A.; Nussinov, R.; Keskin, O.
  3. Nature Protocols. 2011, Sep; 6(9): 1341-1354.
  1. 3.   High recombination rates and hotspots in a Plasmodium falciparum genetic cross
  2. Jiang, H. Y.; Li, N.; Gopalan, V.; Zilversmit, M. M.; Varma, S.; Nagarajan, V.; Li, J.; Mu, J. B.; Hayton, K.; Henschen, B.; Yi, M.; Stephens, R.; McVean, G.; Awadalla, P.; Wellems, T. E.; Su, X. Z.
  3. Genome Biology. 2011, Apr 4; 12(4): 14.
  1. 4.   Comparing interfacial dynamics in protein-protein complexes: an elastic network approach
  2. Zen, A.; Micheletti, C.; Keskin, O.; Nussinov, R.
  3. Bmc Structural Biology. 2010, Aug; 10: 13.
  1. 5.   CCRXP: exploring clusters of conserved residues in protein structures
  2. Ahmad, S.; Keskin, O.; Mizuguchi, K.; Sarai, A.; Nussinov, R.
  3. Nucleic Acids Research. 2010, Jul; 38: W398-W401.
  1. 6.   Protein-DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins
  2. Ahmad, S.; Keskin, O.; Sarai, A.; Nussinov, R.
  3. Nucleic Acids Research. 2008 36(18): 5922-5932.
  1. 7.   Restricted mobility of conserved residues in protein-protein interfaces in molecular simulations
  2. Yogurtcu, O. N.; Erdemli, S. B.; Nussinov, R.; Turkay, M.; Keskin, O.
  3. Biophysical Journal. 2008 94(9): 3475-3485.
  1. 8.   FireDock: Fast interaction refinement in molecular docking
  2. Andrusier, N.; Nussinov, R.; Wolfson, H. J.
  3. Proteins-Structure Function and Bioinformatics. 2007, Oct; 69(1): 139-159.
  1. 9.   Towards drugs targeting multiple proteins in a systems biology approach
  2. Keskin, O.; Gursoy, A.; Ma, B.; Nussinov, R.
  3. Current Topics in Medicinal Chemistry. 2007 7(10): 943-951.
  1. 10.   Association of putative concave protein-binding sites with the fluctuation behavior of residues
  2. Ertekin, A.; Nussinov, R.; Haliloglu, T.
  3. Protein Science. 2006, Oct; 15(10): 2265-2277.
  1. 11.   Nucleotide excision repair and template-independent addition by HIV-1 reverse transcriptase in the presence of nucleocapsid protein
  2. Bampi, C.; Bibillo, A.; Wendeler, M.; Divita, G.; Gorelick, R. J.; Le Grice, S. F. J.; Darlix, J. L.
  3. Journal of Biological Chemistry. 2006, Apr; 281(17): 11736-11743.
  1. 12.   Protein-protein interactions: organization, cooperativity and mapping in a bottom-up Systems Biology approach
  2. Keskin, O.; Ma, B. Y.; Rogale, K.; Gunasekaran, K.; Nussinov, R.
  3. Physical Biology. 2005, JUN; 2(2): S24-S35.
  1. 13.   The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern
  2. De La Vega, F. M.; Isaac, H.; Collins, A.; Scafe, C. R.; Halldorsson, B. V.; Su, X. P.; Lippert, R. A.; Wang, Y.; Laig-Webster, M.; Koehler, R. T.; Ziegle, J. S.; Wogan, L. T.; Stevens, J. F.; Leinen, K. M.; Olson, S. J.; Guegler, K. J.; You, X. Q.; Xu, L. H.; Hemken, H. G.; Kalush, F.; Itakura, M.; Zheng, Y.; de The, G.; O'Brien, S. J.; Clark, A. G.; Istrail, S.; Hunkapiller, M. W.; Spier, E. G.; Gilbert, D. A.
  3. Genome Research. 2005, APR; 15(4): 454-462.
  1. 14.   Large-scale molecular characterization of adeno-associated virus vector integration in mouse liver
  2. Nakai, H.; Wu, X. L.; Fuess, S.; Storm, T. A.; Munroe, D.; Montini, E.; Burgess, S. M.; Grompe, M.; Kay, M. A.
  3. Journal of Virology. 2005, MAR; 79(6): 3606-3614.
  1. 15.   How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues
  2. Haliloglu, T.; Keskin, O.; Ma, B. Y.; Nussinov, R.
  3. Biophysical Journal. 2005, MAR; 88(3): 1552-1559.
  1. 16.   In the quest for stable rescuing mutants of p53: Computational mutagenesis of flexible loop L1
  2. Pan, Y. P.; Ma, B. Y.; Venkataraghavan, R. B.; Levine, A. J.; Nussinov, R.
  3. Biochemistry. 2005, FEB 8; 44(5): 1423-1432.
  1. 17.   Magnitude of the hydrophobic effect at central versus peripheral sites in protein-protein interfaces
  2. Li, Y. L.; Huang, Y. P.; Swaminathan, C. P.; Smith-Gill, S. J.; Mariuzza, R. A.
  3. Structure. 2005, FEB; 13(2): 297-307.
  1. 18.   Favorable scaffolds: proteins with different sequence, structure and function may associate in similar ways
  2. Keskin, O.; Nussinov, R.
  3. Protein Engineering Design & Selection. 2005, JAN; 18(1): 11-24.
  1. 19.   Hot regions in protein-protein interactions: The organization and contribution of structurally conserved hot spot residues
  2. Keskin, O.; Ma, B. Y.; Nussinov, R.
  3. Biophysical Journal. 2005, JAN; 88(1, Part 2, Suppl. S): 5A-5A.
  1. 20.   Protein-protein interactions: Hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: Implications for docking
  2. Li, X.; Keskin, O.; Ma, B. Y.; Nussinov, R.; Liang, J.
  3. Journal of Molecular Biology. 2004, NOV 26; 344(3): 781-795.
  1. 21.   Predicting molecular interactions in silico: II. Protein- protein and protein-drug docking
  2. Schneidman-Duhovny, D.; Nussinov, R.; Wolfson, H. J.
  3. Current Medicinal Chemistry. 2004 11(1): 91-107.
  1. 22.   Interfacial pockets, structurally conserved residues, and energetic hot spots in protein-protein interactions
  2. Li, X.; Keskin, O.; Ma, B. Y.; Nussinov, R.; Liang, J.
  3. Biophysical Journal. 2004 86(1, Part 2 Suppl. S): 301A-301A.
  1. 23.   Justified chauvinism: advances in defining meiotic recombination through sperm typing
  2. Carrington, M.; Cullen, M.
  3. Trends in Genetics. 2004 20(4): 196-205.
  1. 24.   A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications
  2. Keskin, O.; Tsai, C. J.; Wolfson, H.; Nussinov, R.
  3. Protein Science. 2004 13(4): 1043-1055.
  1. 25.   Protein-protein interactions: Coupling of structurally conserved residues and of hot spots across interfaces. implications for docking
  2. Halperin, I.; Wolfson, H.; Nussinov, R.
  3. Structure. 2004 12(6): 1027-1038.
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