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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.   Co-crystal structure of the iMango-III fluorescent RNA aptamer using an X-ray free-electron laser
  2. Trachman, Robert J; Stagno,Jason; Conrad, Chelsie; Jones, Christopher P; Fischer, Pontus; Meents, Alke; Wang, Yun Xing; Ferré-D'Amaré, Adrian R
  3. Acta crystallographica. Section F, Structural biology communications. 2019, Aug 01; 75(Pt 8): 547-551.
  1. 3.   Co-crystal structure of the Fusobacterium ulcerans ZTP riboswitch using an X-ray free-electron laser
  2. Jones, Christopher; Tran, Brandon; Conrad, Chelsie; Stagno,Jason; Trachman, Robert; Fischer, Pontus; Meents, Alke; Ferre-D'Amare, Adrian
  3. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS. 2019, Jul; 75(Part 7): 496-500.
  1. 4.   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. 5.   PATHOLOGIC LESIONS IN CHIMPANZEES (PAN TROGYLODYTES SCHWEINFURTHII) FROM GOMBE NATIONAL PARK, TANZANIA, 2004-2010
  2. Terio, K. A.; Kinsel, M. J.; Raphael, J.; Mlengeya, T.; Lipende, I.; Kirchhoff, C. A.; Gilagiza, B.; Wilson, M. L.; Kamenya, S.; Estes, J. D.; Keele, B. F.; Rudicell, R. S.; Liu, W. M.; Patton, S.; Collins, A.; Hahn, B. H.; Travis, D. A.; Lonsdorf, E. V.
  3. Journal of Zoo and Wildlife Medicine. 2011, Dec; 42(4): 597-607.
  1. 6.   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. 7.   Enhancement of 5-Aminolevulinic acid-induced oxidative stress on two cancer cell lines by gold nanoparticles
  2. Ito, S.; Miyoshi, N.; Degraff, W. G.; Nagashima, K.; Kirschenbaum, L. J.; Riesz, P.
  3. Free Radical Research. 2009 43(12): 1214-1224.
  1. 8.   Integrated molecular profiling of SOD2 expression in multiple myeloma
  2. Hurt, E. M.; Thomas, S. B.; Peng, B. J.; Farrar, W. L.
  3. Blood. 2007, May; 109(9): 3953-3962.
  1. 9.   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. 10.   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. 11.   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. 12.   Plagues and adaptation: Lessons from the Felidae models for SARS and AIDS
  2. O'Brien, S. J.; Troyer, J. L.; Roelke, M.; Marker, L.; Pecon-Slattery, J.
  3. Biological Conservation. 2006, Aug; 131(2): 255-267.
  1. 13.   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. 14.   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. 15.   Seroprevalence and genomic divergence of circulating strains of Feline immunodeficiency virus among Felidae and Hyaenidae species
  2. Troyer, J. L.; Pecon-Slattery, J.; Roelke, M. E.; Johnson, W.; Vande Woude, S.; Vazquez-Salat, N.; Brown, M.; Frank, L.; Woodroffe, R.; Winterbach, C.; Winterbach, H.; Hemson, G.; Bush, M.,; Alexander, K. A.; Revilla, E.; O'Brien, S. J.
  3. Journal of Virology. 2005, JUL; 79(13): 8282-8294.
  1. 16.   Epigenetic silencing of manganese superoxide dismutase (SOD-2) in KAS 6/1 human multiple myeloma cells increases cell proliferation
  2. Hodge, D. R.; Peng, B.; Pompeia, C.; Thomas, S.; Cho, E.; Clausen, P. A.; Marquez, V. E.; Farrar, W. L.
  3. Cancer Biology & Therapy. 2005, May; 4(5): 585-592.
  1. 17.   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. 18.   Cytotoxicity of RH1: NAD(P)H : quinone acceptor oxidoreductase (NQO1)-independent oxidative stress and apoptosis induction
  2. Tudor, G.; Alley, M.; Nelson, C. M.; Huang, R. L.; Covell, D. G.; Gutierrez, P.; Sausville, E. A.
  3. Anti-Cancer Drugs. 2005 16(4): 381-391.
  1. 19.   Big cat genomics
  2. O'Brien, S. J.; Johnson, W. E.
  3. Annual review of genomics and human genetics. 2005 6: 407-429.
  1. 20.   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. 21.   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. 22.   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. 23.   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. 24.   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. 25.   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.
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