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  1. 1.   The Enolization Chemistry of a Thioester-Dependent Racemase: The 1.4 angstrom Crystal Structure of a Reaction Intermediate Complex Characterized by Detailed QM/MM Calculations
  2. Sharma, S.; Bhaumik, P.; Schmitz, W.; Venkatesan, R.; Hiltunen, J. K.; Conzelmann, E.; Juffer, A. H.; Wierenga, R. K.
  3. Journal of Physical Chemistry B. 2012, Mar; 116(11): 3619-3629.
  1. 2.   Enzyme dynamics point to stepwise conformational selection in catalysis
  2. Ma, B. Y.; Nussinov, R.
  3. Current Opinion in Chemical Biology. 2010, Oct; 14(5): 652-659.
  1. 3.   Reaction Mechanism of Glutamate Carboxypeptidase II Revealed by Mutagenesis, X-ray Crystallography, and Computational Methods
  2. Klusak, V.; Barinka, C.; Plechanovova, A.; Mlcochova, P.; Konvalinka, J.; Rulisek, L.; Lubkowski, J.
  3. Biochemistry. 2009 48(19): 4126-4138.
  1. 4.   A permissive secondary structure-guided superposition tool for clustering of protein fragments toward protein structure prediction via fragment assembly
  2. Wainreb, G.; Haspel, N.; Wolfson, H. J.; Nussinov, R.
  3. Bioinformatics. 2006, Jun; 22(11): 1343-1352.
  1. 5.   Antibody-based inhibitors of HIV infection
  2. Choudhry, V.; Zhang, M. Y.; Dimitrova, D.; Prabakaran, P.; Dimitrov, A. S.; Fouts, T. R.; Dimitrov, D. S.
  3. Expert Opinion on Biological Therapy. 2006, MAY; 6(5): 523-531.
  1. 6.   Computational study of a transition state analog of phosphoryl transfer in the Ras-RasGAP complex: AlFx versus MgF3
  2. Grigorenko, B. L.; Nemukhin, A. V.; Cachau, R. E.; Topol, I. A.; Burt, S. K.
  3. Journal of Molecular Modeling. 2005, NOV; 11(6): 503-508.
  1. 7.   Enhancement of antineoplastic action of 5-aza-2'-deoxycytidine by zebularine on L1210 leukemia
  2. Lemaire, M.; Momparler, L. F.; Bernstein, M. L.; Marquez, V. E.; Momparler, R. L.
  3. Anti-Cancer Drugs. 2005, MAR; 16(3): 301-308.
  1. 8.   Recognition of binding patterns common to a set of protein structures
  2. Shatsky, M.; Shulman-Peleg, A.; Nussinov, R.; Wolfson, H. J.
  3. Research in Computational Molecular Biology, Proceedings. 2005 3500: 440-455.
  1. 9.   Fourier transform ion cyclotron resonance MS reveals the presence of a water molecule in an enzyme transition-state analogue complex
  2. Borchers, C. H.; Marquez, V. E.; Schroeder, G. K.; Short, S. A.; Snider, M. J.; Speir, J. P.; Wolfenden, R.
  3. Proceedings of the National Academy of Sciences of the United States of America. 2004, OCT 26; 101(43): 15341-15345.
  1. 10.   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. 11.   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. 12.   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. 13.   PROSIT: Pseudo-Rotational Online Service and Interactive Tool, applied to a conformational survey of nucleosides and nucleotides
  2. Sun, G.; Voigt, J. H.; Filippov, I. V.; Marquez, V. E.; Nicklaus, M. C.
  3. Journal of Chemical Information and Computer Sciences. 2004, SEP-OCT; 44(5): 1752-1762.
  1. 14.   HIV-1 protease variants from 100-fold drug resistant clinical isolates: expression, purification, and crystallization
  2. Vickrey, J. F.; Logsdon, B. C.; Proteasa, G.; Palmer, S.; Winters, M. A.; Merigan, T. C.; Kovari, L. C.
  3. Protein Expression and Purification. 2003 28(1): 165-172.
  1. 15.   Structure-based design of AIDS drugs and the development of resistance
  2. Wlodawer, A.
  3. Vox Sanguinis. 2002 83(Suppl. 1): 23-26.
  1. 16.   Thermal unfolding molecular dynamics simulation of Escherichia coli dihydrofolate reductase: Thermal stability of protein domains and unfolding pathway
  2. Sham, Y. Y.; Ma, B. Y.; Tsai, C. J.; Nussinov, R.
  3. Proteins-Structure Function and Genetics. 2002 46(3): 308-320.
  1. 17.   Rational approach to AIDS drug design through structural biology
  2. Wlodawer, A.
  3. Annual Review of Medicine. 2002 53: 595-614.
  1. 18.   Point mutations and sequence variability in proteins. Redistributions of preexisting populations
  2. Sinha, N.; Nussinov, R.
  3. Proceedings of the National Academy of Sciences of the United States of America. 2001 98(6): 3139-3144.
  1. 19.   Molecular dynamics simulation of Escherichia coli dihydrofolate reductase and its protein fragments: Relative stabilities in experiment and simulations
  2. Sham, Y. Y.; Ma, B. Y.; Tsai, C. J.; Nussinov, R.
  3. Protein Science. 2001 10(1): 135-148.
  1. 20.   The building block folding model and the kinetics of protein folding
  2. Tsai, C. J.; Nussinov, R.
  3. Protein Engineering. 2001 14(10): 723-733.
  1. 21.   Inhibitor complexes of the Pseudomonas serine-carboxyl proteinase
  2. Wlodawer, A.; Li, M.; Gustchina, A.; Dauter, Z.; Uchida, K.; Oyama, H.; Goldfarb, N. E.; Dunn, B. M.; Oda, K.
  3. Biochemistry. 2001 40(51): 15602-15611.
  1. 22.   Transient, highly populated, building blocks folding model
  2. Tsai, C. J.; Nussinov, R.
  3. Cell Biochemistry and Biophysics. 2001 34(2): 209-235.
  1. 23.   Does the interconversion of polysulfur compounds proceed via hypervalent intermediates? - An ab initio MO study
  2. Steudel, R.; Steudel, Y.; Miaskiewicz, K.
  3. Chemistry-a European Journal. 2001 7(15): 3281-3290.
  1. 24.   Molecular dynamics simulations of a beta-hairpin fragment of protein G: Balance between side-chain and backbone forces
  2. Ma, B. Y.; Nussinov, R.
  3. Journal of Molecular Biology. 2000 296(4): 1091-1104.
  1. 25.   Computational studies of the domain movement and the catalytic mechanism of thymidine phosphorylase
  2. Rick, S. W.; Abashkin, Y. G.; Hilderbrandt, R. L.; Burt, S. K.
  3. Proteins. 1999 37(2): 242-252.
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