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  1. 1.   Duplicate entries in the Protein Data Bank: how to detect and handle them
  2. Wlodawer,Alexander; Dauter, Zbigniew; Rubach, Pawel; Minor, Wladek; Jaskolski, Mariusz; Jiang, Ziqiu; Jeffcott, William; Anosova, Olga; Kurlin, Vitaliy
  3. Acta Crystallographica. Section D, Structural Biology. 2025, Apr 01;
  1. 2.   Two independent routes of post-translational chemistry in fluorescent protein FusionRed
  2. Muslinkina,Liya; Pletnev, Vladimir Z; Pletneva, Nadya V; Ruchkin, Dmitry A; Kolesov, Danila V; Bogdanov, Alexey M; Kost, Lubov A; Rakitina, Tatiana V; Agapova, Yulia K; Shemyakina, Irina I; Chudakov, Dmitry M; Pletnev, Sergei
  3. International journal of biological macromolecules. 2020, JUL 15; 155: 551-559.
  1. 3.   SymmRef: A flexible refinement method for symmetric multimers
  2. Mashiach-Farkash, E.; Nussinov, R.; Wolfson, H. J.
  3. Proteins-Structure Function and Bioinformatics. 2011, Sep; 79(9): 2607-2623.
  1. 4.   An integrated suite of fast docking algorithms
  2. Mashiach, E.; Schneidman-Duhovny, D.; Peri, A.; Shavit, Y.; Nussinov, R.; Wolfson, H. J.
  3. Proteins-Structure Function and Bioinformatics. 2010, Nov; 78(15): 3197-3204.
  1. 5.   NCAD, a Database Integrating the Intrinsic Conformational Preferences of Non-Coded Amino Acids
  2. Revilla-Lopez, G.; Torras, J.; Curco, D.; Casanovas, J.; Calaza, M. I.; Zanuy, D.; Jimenez, A. I.; Cativiela, C.; Nussinov, R.; Grodzinski, P.; Aleman, C.
  3. Journal of Physical Chemistry B. 2010, Jun; 114(21): 7413-7422.
  1. 6.   Fiber Dock: Flexible induced-fit backbone refinement in molecular docking
  2. Mashiach, E.; Nussinov, R.; Wolfson, H. J.
  3. Proteins-Structure Function and Bioinformatics. 2010, May; 78(6): 1503-1519.
  1. 7.   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. 8.   The energy landscape of a selective tumor-homing pentapeptide
  2. Zanuy, D.; Flores-Ortega, A.; Casanovas, J.; Curco, D.; Nussinov, R.; Aleman, C.
  3. Journal of Physical Chemistry B. 2008 112(29): 8692-8700.
  1. 9.   How different are structurally flexible and rigid binding sites? Sequence and structural features discriminating proteins that do and do not undergo conformational change upon ligand binding
  2. Gunasekaran, K.; Nussinov, R.
  3. Journal of Molecular Biology. 2007, Jan; 365(1): 257-273.
  1. 10.   Examining Ty3 polypurine tract structure and function by nucleoside analog interference
  2. Dash, C.; Marino, J. P.; Le Grice, S. F. J.
  3. Journal of Biological Chemistry. 2006, FEB 3; 281(5): 2773-2783.
  1. 11.   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. 12.   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. 13.   Determining a helical protein structure using peptide pixels
  2. Walsh, J. D.; Kuszweski, J.; Wang, Y. X.
  3. Journal of Magnetic Resonance. 2005, NOV; 177(1): 155-159.
  1. 14.   Effect of posttranscriptional regulatory elements on transgene expression and virus production in the context of retrovirus vectors
  2. Hlavaty, J.; Schittmayer, M.; Stracke, A.; Jandl, G.; Knapp, E.; Felber, B. K.; Salmons, B.; Gunzburg, W. H.; Renner, M.
  3. Virology. 2005, OCT 10; 341(1): 1-11.
  1. 15.   Reconstruction of the conserved beta-bulge in mammalian defensins using D-amino acids
  2. Xie, C.; Prahl, A.; Ericksen, B.; Wu, Z. B.; Zeng, P. Y.; Li, X. Q.; Lu, W. Y.; Lubkowski, J.; Lu, W. Y.
  3. Journal of Biological Chemistry. 2005, SEP 23; 280(38): 32921-32929.
  1. 16.   Isolation and characterization of novel cyclotides from Viola hederaceae - Solution structure and anti-HIV activity of vhl-1, a leaf-specific expressed cyclotide
  2. Chen, B.; Colgrave, M. L.; Daly, N. L.; Rosengren, K. J.; Gustafson, K. R.; Craik, D. J.
  3. Journal of Biological Chemistry. 2005, JUN 10; 280(23): 22395-22405.
  1. 17.   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. 18.   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. 19.   Investigating HIV-1 polypurine tract geometry via targeted insertion of abasic lesions in the (-)-DNA template and (+)-RNA primer
  2. Yi-Brunozzi, H. Y.; Le Grice, S. F. J.
  3. Journal of Biological Chemistry. 2005, MAY 20; 280(20): 20154-20162.
  1. 20.   Detection of C ' C-alpha correlations in proteins using a new time- and sensitivity-optimal experiment
  2. Lee, D.; Vogeli, B.; Pervushin, K.
  3. Journal of Biomolecular Nmr. 2005, APR; 31(4): 273-278.
  1. 21.   Structure of circulin B and implications for antimicrobial activity of the cyclotides
  2. Koltay, A.; Daly, N. L.; Gustafson, K. R.; Craik, D. J.
  3. International Journal of Peptide Research and Therapeutics. 2005, MAR; 11(1): 99-106.
  1. 22.   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. 23.   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. 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.   Anti-HIV cyclotides
  2. Gustafson, K. R.; McKee, T. C.; Bokesch, H. R.
  3. Current Protein & Peptide Science. 2004, OCT; 5(5): 331-340.
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