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  1. 1.   Understanding antibody-antigen associations by molecular dynamics simulations: Detection of important intra- and inter-molecular salt bridges
  2. Sinha, N.; Li, Y. L.; Lipschultz, C. A.; Smith-Gill, S. J.
  3. Cell Biochemistry and Biophysics. 2007 47(3): 361-375.
  1. 2.   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. 3.   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. 4.   The stability and free energy landscape of an amyloid-forming peptide DFNKF from the human calcitonin in explicit water
  2. Tsai, H. H. G.; Tsai, C. J.; Ma, B.; Gunasekaran, K.; Zanuy, D.; Nussinov, R.
  3. Biophysical Journal. 2004 86(1, Part 2 Suppl. S): 412A-412A.
  1. 5.   Mechanistic insights into the kinetics of HIV-1 nucleocapsid protein-facilitated tRNA annealing to the primer binding site
  2. Hargittai, M. R. S.; Gorelick, R. J.; Rouzina, L.; Musier-Forsyth, K.
  3. Journal of Molecular Biology. 2004 337(4): 951-968.
  1. 6.   Different roles of electrostatics in heat and in cold: Adaptation by citrate synthase
  2. Kumar, S.; Nussinov, R.
  3. Chembiochem. 2004 5(3): 280-290.
  1. 7.   Subatomic and atomic crystallographic studies of aldose reductase: implications for inhibitor binding
  2. Podjarny, A.; Cachau, R. E.; Schneider, T.; Van Zandt, M.; Joachimiak, A.
  3. Cellular and Molecular Life Sciences. 2004 61(7-8): 763-773.
  1. 8.   Close-range electrostatic interactions in proteins
  2. Kumar, S.; Nussinov, R.
  3. Chembiochem. 2002 3(7): 604-617.
  1. 9.   Acidity of organic molecules in the gas phase and in aqueous solvent
  2. Topol, I. A.; Tawa, G. J.; Caldwell, R. A.; Eissenstat, M. A.; Burt, S. K.
  3. Journal of Physical Chemistry A. 2000 104(42): 9619-9624.
  1. 10.   HIV protease: Enzyme function and drug resistance
  2. Gulnik, S.; Erickson, J. W.; Xie, D.
  3. Vitamins and Hormones - Advances in Research and Applications, Vol 58. 2000 58: 213-256.
  1. 11.   Explicit and implicit water simulations of a beta-hairpin peptide
  2. Ma, B. Y.; Nussinov, R.
  3. Proteins. 1999 37(1): 73-87.
  1. 12.   On the structure and thermodynamics of solvated monoatomic ions using a hybrid solvation model
  2. Topol, I. A.; Tawa, G. J.; Burt, S. K.; Rashin, A. A.
  3. Journal of Chemical Physics. 1999 111(24): 10998-11014.
  1. 13.   Prediction of binding affinities for TIBO inhibitors of HIV-1 reverse transcriptase using Monte Carlo simulations in a linear response method
  2. Smith, R. H.; Jorgensen, W. L.; Tirado-Rives, J.; Lamb, M. L.; Janssen, P. A. J.; Michejda, C. J.; Smith, M. B. K.
  3. Journal of Medicinal Chemistry. 1998 41(26): 5272-5286.
  1. 14.   Inhibitors of Hiv-1 Protease - a Major Success of Structure-Assisted Drug Design
  2. Wlodawer, A.; Vondrasek, J.
  3. Annual Review of Biophysics and Biomolecular Structure. 1998 27: 249-284.
  1. 15.   A Monte Carlo Method For Finding Important Ligand Fragments From Receptor Data
  2. Burt, S.; Hutchins, C.; Zielinski, P. J.
  3. Journal of Computer-Aided Molecular Design. 1997 11(3): 243-255.
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