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  1. 1.   Induced fit, conformational selection and independent dynamic segments: an extended view of binding events
  2. Csermely, P.; Palotai, R.; Nussinov, R.
  3. Trends in Biochemical Sciences. 2010, Oct; 35(10): 539-546.
  1. 2.   Application of ring-closing metathesis macrocyclization to the development of Tsg101-binding antagonists
  2. Liu, F.; Stephen, A. G.; Waheed, A. A.; Freed, E. O.; Fisher, R. J.; Burke, T. R.
  3. Bioorganic & Medicinal Chemistry Letters. 2010, Jan; 20(1): 318-321.
  1. 3.   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. 4.   A new perspective in the Lewis acid catalyzed ring opening of epoxides. Theoretical study of some complexes of methanol, acetic acid, dimethyl ether, diethyl ether, and ethylene oxide with boron trifluoride
  2. Saenz, P.; Cachau, R. E.; Seoane, G.; Kieninger, M.; Ventura, O. N.
  3. Journal of Physical Chemistry A. 2006, Oct; 110(41): 11734-11751.
  1. 5.   Catalytic role of proton transfers in the formation of a tetrahedral adduct in a serine carboxyl peptidase
  2. Guo, H. B.; Wlodawer, A.; Nakayama, T.; Xu, Q.; Guo, H.
  3. Biochemistry. 2006, Aug; 45(30): 9129-9137.
  1. 6.   Structural mimicry of CD4 by a cross-reactive HIV-1 neutralizing antibody with CDR-H2 and H3 containing unique motifs
  2. Prabakaran, P.; Gan, J. H.; Wu, Y. Q.; Zhang, M. Y.; Dimitrov, D. S.; Ji, X. H.
  3. Journal of Molecular Biology. 2006, MAR 17; 357(1): 82-99.
  1. 7.   Atomic-level description of amyloid beta-dimer formation
  2. Gnanakaran, S.; Nussinov, R.; Garcia, A. E.
  3. Journal of the American Chemical Society. 2006, Feb; 128(7): 2158-2159.
  1. 8.   Structural and dynamical classification of RNA single-base bulges for nanostructure design
  2. Hastings, W. A.; Yingling, Y. G.; Chirikjian, G. S.; Shapiro, B. A.
  3. Journal of Computational and Theoretical Nanoscience. 2006, FEB; 3(1): 63-77.
  1. 9.   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. 10.   Binding affinity difference induced by the stereochemistry of the sulfoxide bridge of the cyclic peptide inhibitors of Grb2-SH2 domain: NMR studies for the structural origin
  2. Shi, Y. H.; Song, Y. L.; Lin, D. H.; Tan, J. Z.; Roller, P. P.; Li, Q.; Long, Y. Q.; Song, G. Q.
  3. Biochemical and Biophysical Research Communications. 2005, MAY 20; 330(4): 1254-1261.
  1. 11.   Dynamic behavior of the telomerase RNA hairpin structure and its relationship to dyskeratosis congenita
  2. Yingling, Y. G.; Shapiro, B. A.
  3. Journal of Molecular Biology. 2005, APR 22; 348(1): 27-42.
  1. 12.   Mutation of arginine 228 to lysine enhances the glucosyltransferase activity of bovine beta-1,4-galactosyltransferase I
  2. Ramakrishnan, B.; Boeggeman, E.; Qasba, P. K.
  3. Biochemistry. 2005, MAR 8; 44(9): 3202-3210.
  1. 13.   A comparative study of amyloid fibril formation by residues 15-19 of the human calcitonin hormone: A single beta-sheet model with a small hydrophobic core
  2. Haspel, N.; Zanuy, D.; Ma, B. Y.; Wolfson, H.; Nussinov, R.
  3. Journal of Molecular Biology. 2005, FEB 4; 345(5): 1213-1227.
  1. 14.   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. 15.   Small nonphosphorylated Grb2-SH2 domain antagonists evaluated by surface resonance plasmon technology
  2. Lung, F. D. T.; Chang, C. W.; Chong, M. C.; Liou, C. C.; Li, P.; Peach, M. L.; Nicklaus, M. C.; Lou, B. S.; Roller, P. P.
  3. Peptide Science (Biopolymers). 2005 80(5): 628-635.
  1. 16.   Crystal structure of human glutathione S-transferase A3-3 and mechanistic implications for its high steroid isomerase activity
  2. Gu, Y. J.; Guo, J. X.; Pal, A.; Pan, S. S.; Zimniak, P.; Singh, S. V.; Ji, X. H.
  3. Biochemistry. 2004, DEC 21; 43(50): 15673-15679.
  1. 17.   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. 18.   Solution structure of the pseudo-5 ' splice site of a retroviral splicing suppressor
  2. Cabello-Villegas, J.; Giles, K. E.; Soto, A. M.; Yu, P.; Mougin, A.; Beemon, K. L.; Wang, Y. X.
  3. Rna-a Publication of the Rna Society. 2004, SEP; 10(9): 1388-1398.
  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.   Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by Hhal methyltransferase
  2. Horton, J. R.; Ratner, G.; Banavali, N. K.; Huang, N.; Choi, Y.; Maier, M. A.; Marquez, V. E.; Mackerell, A. D.; Cheng, X. D.
  3. Nucleic Acids Research. 2004 32(13): 3877-3886.
  1. 21.   Predicting molecular interactions in silico: I. A guide to pharmacophore identification and its applications to drug design
  2. Dror, O.; Shulman-Peleg, A.; Nussinov, R.; Wolfson, H. J.
  3. Current Medicinal Chemistry. 2004 11(1): 71-90.
  1. 22.   De novo design and characterization of a helical hairpin eicosapeptide: Emergence of an anion receptor in the linker region
  2. Rudresh; Ramakumar, S.; Ramagopal, U. A.; Inai, Y.; Goel, S.; Sahal, D.
  3. Structure. 2004 12(3): 389-396.
  1. 23.   PCR amplification of DNA containing non-standard base pairs by variants of reverse transcriptase from Human Immunodeficiency Virus-1
  2. Sismour, A. M.; Lutz, S.; Park, J. H.; Lutz, M. J.; Boyer, P. L.; Hughes, S. H.; Benner, S. A.
  3. Nucleic Acids Research. 2004 32(2): 728-735.
  1. 24.   Ultrahigh resolution drug design I: Details of interactions in human aldose reductase-inhibitor complex at 0.66 angstrom
  2. Howard, E. I.; Sanishvili, R.; Cachau, R. E.; Mitschler, A.; Chevrier, B.; Barth, P.; Lamour, V.; Van Zandt, M.; Sibley, E.; Bon, C.; Moras, D.; Schneider, T. R.; Joachimiak, A.; Podjarny, A.
  3. Proteins-Structure Function and Bioinformatics. 2004 55(4): 792-804.
  1. 25.   Transient, highly populated, building blocks folding model
  2. Tsai, C. J.; Nussinov, R.
  3. Cell Biochemistry and Biophysics. 2001 34(2): 209-235.
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