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  1. 1.   Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis
  2. Nguyen, Phuong H.; Ramamoorthy, Ayyalusamy; Sahoo, Bikash R.; Zheng, Jie; Faller, Peter; Straub, John E.; Dominguez, Laura; Shea, Joan-Emma; Dokholyan, Nikolay; De Simone, Alfonso; Ma, Buyong; Nussinov,Ruth; Najafi, Saeed; Ngo, Son Tung; Loquet, Antoine; Chiricotto, Mara; Ganguly, Pritam; McCarty, James; Li, Mai Suan; Hall, Carol; Wang, Yiming; Miller, Yifat; Melchionna, Simone; Habenstein, Birgit; Timr, Stepan; Chen, Jiaxing; Hnath, Brianna; Strodel, Birgit; Kayed, Rakez; Lesne, Sylvain; Wei, Guanghong; Sterpone, Fabio; Doig, Andrew J.; Derreumaux, Philippe
  3. Chemical Reviews. 2021, Feb 24; 121(4): 2545-2647.
  1. 2.   Computational Structural Biology: Successes, Future Directions, and Challenges
  2. Nussinov, Ruth; Tsai, Chung-Jung; Shehu, Amarda; Jang, Hyunbum
  3. Molecules (Basel, Switzerland). 2019, Feb 1; 24(3):
  1. 3.   Software and resources for computational medicinal chemistry
  2. Liao, C. Z.; Sitzmann, M.; Pugliese, A.; Nicklaus, M. C.
  3. Future Medicinal Chemistry. 2011, Jun; 3(8): 1057-1085.
  1. 4.   Bridging the gap in RNA structure prediction
  2. Shapiro, B. A.; Yingling, Y. G.; Kasprzak, W.; Bindewald, E.
  3. Current Opinion in Structural Biology. 2007, Apr; 17(2): 157-165.
  1. 5.   Mechanisms of guanosine triphosphate hydrolysis by Ras and Ras-GAP proteins as rationalized by ab initio QM/MM simulations
  2. Grigorenko, B. L.; Nemukhin, A. V.; Shadrina, M. S.; Topol, I. A.; Burt, S. K.
  3. Proteins-Structure Function and Bioinformatics. 2007, Feb; 66(2): 456-466.
  1. 6.   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. 7.   Molecular modeling the reaction mechanism of serine-carboxyl peptidases
  2. Bravaya, K.; Bochenkova, A.; Grigorenko, B.; Topol, I.; Burt, S.; Nemukhin, A.
  3. Journal of Chemical Theory and Computation. 2006, Jul; 2(4): 1168-1175.
  1. 8.   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. 9.   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. 10.   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. 11.   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. 12.   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. 13.   Modeling of serine protease prototype reactions with the flexible effective fragment potential quantum mechanical/molecular mechanical method
  2. Nemukhin, A. V.; Grigorenko, B. L.; Rogov, A. V.; Topol, I. A.; Burt, S. K.
  3. Theoretical Chemistry Accounts. 2004 111(1): 36-48.
  1. 14.   Subatomic and atomic crystallographic studies of aldose reductase: implications for inhibitor binding
  2. Podjarny, A.; Cachau, R. E.; Schneider, T.; Van Zandt, M.; Joachimiak, A.
  3. Cellular and Molecular Life Sciences. 2004 61(7-8): 763-773.
  1. 15.   Solution conformations of wild-type and mutated Bak BH3 peptides via dynamical conformational sampling and implication to their binding to antiapoptotic Bcl-2 proteins
  2. Yang, C. Y.; Nikolovska-Coleska, Z.; Li, P.; Roller, P.; Wang, S. M.
  3. Journal of Physical Chemistry B. 2004 108(4): 1467-1477.
  1. 16.   Theoretical studies on the hydrolysis of mono-phosphate and tri-phosphate in gas phase and aqueous solution
  2. Wang, Y. N.; Topol, I. A.; Collins, J. R.; Burt, S. K.
  3. Journal of the American Chemical Society. 2003 125(43): 13265-13273.
  1. 17.   EVEBAT: A fast strategy for the examination of the empty space in polymer matrices
  2. Curco, D.; Zanuy, D.; Aleman, C.
  3. Journal of Computational Chemistry. 2003 24(10): 1208-1214.
  1. 18.   On the origin of potential barrier for the reaction OH-+CO2 -> HCO3- in water: Studies by using continuum and cluster solvation methods
  2. Nemukhin, A. V.; Topol, I. A.; Grigorenko, B. L.; Burt, S. K.
  3. Journal of Physical Chemistry B. 2002 106(7): 1734-1740.
  1. 19.   Rational approach to AIDS drug design through structural biology
  2. Wlodawer, A.
  3. Annual Review of Medicine. 2002 53: 595-614.
  1. 20.   Analysis of ligand-macromolecule contacts: Computational methods
  2. Pattabiraman, N.
  3. Current Medicinal Chemistry. 2002 9(5): 609-621.
  1. 21.   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. 22.   Monte Carlo calculations on HIV-1 reverse transcriptase complexed with the non-nucleoside inhibitor 8-Cl TIBO: contribution of the L100I and Y181C variants to protein stability and biological activity
  2. Smith, M. B. K.; Lamb, M. L.; Tirado-Rives, J.; Jorgensen, W. L.; Michejda, C. J.; Ruby, S. K.; Smith, R. H.
  3. Protein Engineering. 2000 13(6): 413-421.
  1. 23.   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. 24.   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. 25.   Explicit and implicit water simulations of a beta-hairpin peptide
  2. Ma, B. Y.; Nussinov, R.
  3. Proteins. 1999 37(1): 73-87.
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