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  1. 1.   Structural host- microbiota interaction networks
  2. Guven-Maiorov, Emine; Tsai, Chung-Jung; Nussinov, Ruth
  3. PLOS COMPUTATIONAL BIOLOGY. 2017, OCT; 13(10):
  1. 2.   Allostery and population shift in drug discovery
  2. Kar, G.; Keskin, O.; Gursoy, A.; Nussinov, R.
  3. Current Opinion in Pharmacology. 2010, Dec; 10(6): 715-722.
  1. 3.   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. 4.   Towards inferring time dimensionality in protein-protein interaction networks by integrating structures: the p53 example
  2. Tuncbag, N.; Kar, G.; Gursoy, A.; Keskin, O.; Nussinov, R.
  3. Molecular Biosystems. 2009 5(12): 1770-1778.
  1. 5.   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. 6.   Topological properties of protein interaction networks from a structural perspective
  2. Gursoy, A.; Keskin, O.; Nussinov, R.
  3. Biochemical Society Transactions. 2008 36: 1398-1403.
  1. 7.   MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions
  2. Shulman-Peleg, A.; Shatsky, M.; Nussinov, R.; Wolfson, H. J.
  3. Nucleic Acids Research. 2008 36: W260-W264.
  1. 8.   Structure and activity of Yersinia pestis 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase as a novel target for the development of antiplague therapeutics
  2. Blaszczyk, J.; Li, Y.; Cherry, S.; Alexandratos, J.; Wu, Y.; Shaw, G.; Tropea, J. E.; Waugh, D. S.; Yan, H. G.; Ji, X. H.
  3. Acta Crystallographica Section D-Biological Crystallography. 2007, Nov; 63: 1169-1177.
  1. 9.   Three-dimensional structure of yellow fluorescent protein zYFP538 from Zoanthus sp at the resolution 1.8 angstrom
  2. Pletneva, N. V.; Pletnev, S. V.; Chudakov, D. M.; Tikhonova, T. V.; Popov, V. O.; Martynov, V. I.; Wlodawer, A.; Dauter, Z.; Pletnev, V. Z.
  3. Russian Journal of Bioorganic Chemistry. 2007, Jul; 33(4): 390-398.
  1. 10.   Similar binding sites and different partners: Implications to shared proteins in cellular pathways
  2. Keskin, O.; Nussinov, R.
  3. Structure. 2007, Mar; 15(3): 341-354.
  1. 11.   Trp/Met/Phe hot spots in protein-protein interactions: Potential targets in drug design
  2. Ma, B.; Nussinov, R.
  3. Current Topics in Medicinal Chemistry. 2007 7(10): 999-1005.
  1. 12.   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. 13.   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. 14.   Structure and dynamics of micelle-associated human immunodeficiency virus gp41 fusion domain
  2. Jaroniec, C. P.; Kaufman, J. D.; Stahl, S. J.; Viard, M.; Blumenthal, R.; Wingfield, P. T.; Bax, A.
  3. Biochemistry. 2005, DEC 13; 44(49): 16167-16180.
  1. 15.   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. 16.   The contribution of the Trp/Met/Phe residues to physical interactions of p53 with cellular proteins
  2. Ma, B. Y.; Pan, Y. P.; Gunasekaran, K.; Keskin, O.; Venkataraghavan, R. B.; Levine, A. J.; Nussinov, R.
  3. Physical Biology. 2005, JUN; 2(2): S56-S66.
  1. 17.   Comparison of the protein-protein interfaces in the p53-DNA crystal structures: Towards elucidation of the biological interface
  2. Ma, B. Y.; Pan, Y. P.; Gunasekaran, K.; Venkataraghavan, R. B.; Levine, A. J.; Nussinov, R.
  3. Proceedings of the National Academy of Sciences of the United States of America. 2005, MAR 15; 102(11): 3988-3993.
  1. 18.   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. 19.   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. 20.   Multiple docking for protein structure prediction
  2. Inbar, Y.; Wolfson, H. J.; Nussinov, R.
  3. International Journal of Robotics Research. 2005, FEB-MAR; 24(2-3): 131-150.
  1. 21.   MAPPIS: Multiple 3D alignment of protein-protein interfaces
  2. Shulman-Peleg, A.; Shatsky, M.; Nussinov, R.; Wolfson, H. J.
  3. Computational Life Sciences. 2005; 3695 : 91-103.
  1. 22.   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. 23.   Three-dimensional model of the pore form of anthrax protective antigen. Structure and biological implications
  2. Nguyen, T. L.
  3. Journal of Biomolecular Structure & Dynamics. 2004, DEC; 22(3): 253-265.
  1. 24.   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. 25.   Sheathless electrospray ionization interfaces for capillary electrophoresis-mass spectrometric detection - Advantages and limitations
  2. Issaq, H. J.; Janini, G. M.; Chan, K. C.; Veenstra, T. D.
  3. Journal of Chromatography A. 2004, OCT 22; 1053(1-2): 37-42.
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