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  1. 1.   Exploring the energy landscape of a molecular engineered analog of a tumor-homing peptide
  2. Revilla-Lopez, G.; Torras, J.; Nussinov, R.; Aleman, C.; Zanuy, D.
  3. Physical Chemistry Chemical Physics. 2011, Jun 7; 13(21): 9986-9994.
  1. 2.   Conformational Preferences of 1-Amino-2-phenylcyclohexanecarboxylic Acid, a Phenylalanine Cyclohexane Analogue
  2. Aleman, C.; Jimenez, A. I.; Cativiela, C.; Nussinov, R.; Casanovas, J.
  3. Journal of Organic Chemistry. 2009 74(20): 7834-7843.
  1. 3.   Influence of the Dye Presence on the Conformational Preferences of CREKA, a Tumor Homing Linear Pentapeptide
  2. Zanuy, D.; Curco, D.; Nussinov, R.; Aleman, C.
  3. Biopolymers. 2009 92(2): 83-93.
  1. 4.   Intrinsic conformational preferences of C-alpha,C-alpha-dibenzylglycine
  2. Casanovas, J.; Nussinov, R.; Aleman, C.
  3. Journal of Organic Chemistry. 2008 73(11): 4205-4211.
  1. 5.   Conformational Preferences of beta- and gamma-Aminated Proline Analogues
  2. Flores-Ortega, A.; Casanovas, J.; Nussinov, R.; Aleman, C.
  3. Journal of Physical Chemistry B. 2008 112(44): 14045-14055.
  1. 6.   The impact of dyskeratosis congenita mutations on the structure and dynamics of the human telomerase RNA pseudoknot domain
  2. Yingling, Y. G.; Shapiro, B. A.
  3. Journal of Biomolecular Structure & Dynamics. 2007, Feb; 24(4): 303-319.
  1. 7.   Release factors eRF1 and RF2 - A universal mechanism controls the large conformational changes
  2. Ma, B. Y.; Nussinov, R.
  3. Journal of Biological Chemistry. 2004, DEC 17; 279(51): 53875-53885.
  1. 8.   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. 9.   The application of the effective fragment potential method to molecular anion solvation: A study of ten oxyanion-water clusters, A(-)(H2O)(1-4)
  2. Merrill, G. N.; Webb, S. P.
  3. Journal of Physical Chemistry A. 2004 108(5): 833-839.
  1. 10.   QM/MM modeling of the glutathione-hydroxymethyl radical reaction in watery
  2. Nemukhin, A. V.; Grigorenko, B. L.; Topol, I. A.; Burt, S. K.
  3. Physical Chemistry Chemical Physics. 2004 6(5): 1031-1038.
  1. 11.   Effect of polymer concentration on partitioning and molecular recognition in plasticized poly(vinyl chloride)
  2. Zhang, X.; Zhao, H.; Chen, Z.; Nims, R.; Weber, S. G.
  3. Analytical Chemistry. 2003 75(16): 4257-4264.
  1. 12.   Molecular modeling calculations of HIV-1 reverse transcriptase nonnucleoside inhibitors: Correlation of binding energy with biological activity for novel 2-aryl-substituted benzimidazole analogues
  2. Smith, M. B. K.; Hose, B. M.; Hawkins, A.; Lipchock, J.; Farnsworth, D. W.; Rizzo, R. C.; Tirado-Rives, J.; Arnold, E.; Zhang, W.; Hughes, S. H.; Jorgensen, W. L.; Michejda, C. J.; Smith, R. H.
  3. Journal of Medicinal Chemistry. 2003 46(10): 1940-1947.
  1. 13.   A QM/MM approach with effective fragment potentials applied to the dipeptide-water structures
  2. Nemukhin, A. V.; Grigorenko, B. L.; Bochenkova, A. V.; Topol, I. A.; Burt, S. K.
  3. Journal of Molecular Structure-theochem. 2002 581: 167-175.
  1. 14.   Charge distributions in water and ion-water clusters
  2. Rashin, A. A.; Topol, I. A.; Tawa, G. J.; Burt, S. K.
  3. Chemical Physics Letters. 2001 335(3-4): 327-333.
  1. 15.   Molecular dynamics simulations of the denaturation and refolding of an RNA tetraloop
  2. Li, W.; Ma, B. Y.; Shapiro, B. A.
  3. Journal of Biomolecular Structure & Dynamics. 2001 19(3): 381-396.
  1. 16.   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. 17.   Quantum chemical studies of reactions of the cyclic disulfides with the zinc finger domains in the HIV-1 nucleocapsid protein (NCp7)
  2. Topol, I. A.; Nemukhin, A. V.; Chao, M.; Iyer, L. K.; Tawa, G. J.; Burt, S. K.
  3. Journal of the American Chemical Society. 2000 122(29): 7087-7094.
  1. 18.   Calculation of substituent effects on pK(a) values for pyrone and dihydropyrone inhibitors of HIV-1 protease
  2. Topol, I. A.; Burt, S. K.; Rashin, A. A.; Erickson, J. W.
  3. Journal of Physical Chemistry. 2000 104(4): 866-872.
  1. 19.   Explicit and implicit water simulations of a beta-hairpin peptide
  2. Ma, B. Y.; Nussinov, R.
  3. Proteins. 1999 37(1): 73-87.
  1. 20.   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. 21.   Hydrophobic Interactions in Aqueous Urea Solutions With Implications For the Mechanism of Protein Denaturation
  2. Wallqvist, A.; Covell, D. G.; Thirumalai, D.
  3. Journal of the American Chemical Society. 1998 120(2): 427-428.
  1. 22.   Reaction Path and Free Energy Calculations of the Transition Between Alternate Conformations of Hiv-1 Protease
  2. Rick, S. W.; Erickson, J. W.; Burt, S. K.
  3. Proteins. 1998 32(1): 7-16.
  1. 23.   Analysis of Protein-Protein Interactions and the Effects of Amino Acid Mutations On Their Energetics - the Importance of Water Molecules in the Binding Epitope
  2. Covell, D. G.; Wallqvist, A.
  3. Journal of Molecular Biology. 1997 269(2): 281-297.
  1. 24.   Protein Binding Versus Protein Folding - the Role of Hydrophilic Bridges in Protein Associations
  2. Xu, D.; Lin, S. L.; Nussinov, R.
  3. Journal of Molecular Biology. 1997 265(1): 68-84.
  1. 25.   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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