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  1. 1.   Testing beta-helix terminal coils stability by targeted substitutions with non-proteogenic amino acids: A molecular dynamics study
  2. Zanuy, D.; Rodriguez-Ropero, F.; Nussinov, R.; Aleman, C.
  3. Journal of Structural Biology. 2007, Nov; 160(2): 177-189.
  1. 2.   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. 3.   Comprehensive analysis of pathway or functionally related gene expression in the National Cancer Institute's anticancer screen
  2. Huang, R.; Wallqvist, A.; Covell, D. G.
  3. Genomics. 2006, MAR; 87(3): 315-328.
  1. 4.   Structural differentiation of the HIV-1 poly(A) signals
  2. Gee, A. H.; Kasprzak, W.; Shapiro, B. A.
  3. Journal of Biomolecular Structure & Dynamics. 2006, FEB; 23(4): 417-428.
  1. 5.   A systematic multireference perturbation-theory study of the low-lying states of SiC3
  2. Rintelman, J. M.; Gordon, M. S.; Fletcher, G. D.; Ivanic, J.
  3. Journal of Chemical Physics. 2006, JAN 21; 124(3, Art. No. 034303):
  1. 6.   Electronic excitations of the chromophore from the fluorescent protein asFP595 in solutions
  2. Nemukhin, A. V.; Topol, I. A.; Burt, S. K.
  3. Journal of Chemical Theory and Computation. 2006, Mar-Apr; 2(2): 292-299.
  1. 7.   Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A
  2. Park, J. G.; Sill, P. C.; Makiyi, E. F.; Garcia-Sosa, A. T.; Millard, C. B.; Schmidt, J. J.; Pang, Y. P.
  3. Bioorganic & Medicinal Chemistry. 2006, Jan; 14(2): 395-408.
  1. 8.   Dolastatin 11 conformations, analogues and pharmacophore
  2. Ali, M. A.; Bates, R. B.; Crane, Z. D.; Dicus, C. W.; Gramme, M. R.; Hamel, E.; Marcischak, J.; Martinez, D. S.; McClure, K. J.; Nakkiew, P.; Pettit, G. R.; Stessman, C. C.; Sufi, B. A.; Yarick, G. V.
  3. Bioorganic & Medicinal Chemistry. 2005, JUL 1; 13(13): 4138-4152.
  1. 9.   Ligand-induced partitioning of human CXCR1 chemokine receptors with lipid raft microenvironments facilitates G-protein-dependent signaling
  2. Jiao, X. M.; Zhang, N.; Xu, X. H.; Oppenheim, J. J.; Jin, T.
  3. Molecular and Cellular Biology. 2005, JUL; 25(13): 5752-5762.
  1. 10.   Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: Significant role of Asn ladder
  2. Tsai, H. H.; Reches, M.; Tsai, C. J.; Gunasekaran, K.; Gazit, E.; Nussinov, R.
  3. Proceedings of the National Academy of Sciences of the United States of America. 2005, JUN 7; 102(23): 8174-8179.
  1. 11.   Structure, stability, and NMR properties of lower fullerenes C-38-C-50 and azafullerene C44N6
  2. Sun, G. Y.; Nicklaus, M. C.; Xie, R. H.
  3. Journal of Physical Chemistry A. 2005, MAY 26; 109(20): 4617-4622.
  1. 12.   Global transcriptional programs reveal a carbon source foraging strategy by Escherichia coli
  2. Liu, M. Z.; Durfee, T.; Cabrera, J. E.; Zhao, K.; Jin, D. J.; Blattner, F. R.
  3. Journal of Biological Chemistry. 2005, APR 22; 280(16): 15921-15927.
  1. 13.   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. 14.   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. 15.   In vivo HIV-1 rev multimerization in the nucleolus and cytoplasm identified by fluorescence resonance energy transfer
  2. Daelemans, D.; Costes, S. V.; Cho, E. H.; Erwin-Cohen, R. A.; Lockett, S.; Pavlakis, G. N.
  3. Journal of Biological Chemistry. 2004, NOV 26; 279(48): 50167-50175.
  1. 16.   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. 17.   Inhibition of HIV-1 envelope glycoprotein-mediated cell fusion by a DL-amino acid-containing fusion peptide - Possible recognition of the fusion complex
  2. Gerber, D.; Pritsker, M.; Gunther-Ausborn, S.; Johnson, B.; Blumenthal, R.; Shai, Y.
  3. Journal of Biological Chemistry. 2004, NOV 12; 279(46): 48224-48230.
  1. 18.   A structural similarity analysis of double-helical DNA
  2. Gardiner, E. J.; Hunter, C. A.; Lu, X. J.; Willett, P.
  3. Journal of Molecular Biology. 2004, OCT 29; 343(4): 879-889.
  1. 19.   Multiple proton translocation in biomolecular systems: concerted to stepwise transition in a simple model
  2. Kohanoff, J. J.; Cachau, R. E.
  3. Molecular Physics. 2004, MAY 10; 102(9-10): 1007-1014.
  1. 20.   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. 21.   Excitations, optical absorption spectra, and optical excitonic gaps of heterofullerenes. 1. C-60, C59N+, and C48N12: Theory and experiment
  2. Xie, R. H.; Bryant, G. W.; Sun, G. Y.; Nicklaus, M. C.; Heringer, D.; Frauenheim, T.; Manaa, M. R.; Smith, V. H.; Araki, Y.; Ito, O.
  3. Journal of Chemical Physics. 2004 120(11): 5133-5147.
  1. 22.   (Salen)Mn(III) compound as a nonpeptidyl mimic of catalase: DFT study of the metal oxidation by a peroxide molecule
  2. Abashkin, Y. G.; Burt, S. K.
  3. Journal of Physical Chemistry B. 2004 108(8): 2708-2711.
  1. 23.   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. 24.   Theoretical study of the low lying electronic states of oxoX(salen) (X = Mn, Mn-, Fe, and Cr-) complexes
  2. Ivanic, J.; Collins, J. R.; Burt, S. K.
  3. Journal of Physical Chemistry A. 2004 108(12): 2314-2323.
  1. 25.   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.
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