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  1. 1.   Elements in the 5' Untranslated Region of Viral RNA Important for HIV Gag Recognition and Cross-Packaging
  2. Cheng,Zetao; Nikolaitchik,Olga; Duchon,Alice; Rawson, Jonathan M O; Pathak,Vinay; Hu,Wei-Shau
  3. Viruses. 2025, Apr 10; 17(4): 551.
  1. 2.   Design, Synthesis and Biological Evaluation of 2-Phenyl Indole Analogues of OXi8006 as Colchicine Site Inhibitors of Tubulin Polymerization and Vascular Disrupting Agents
  2. Vairin, Rebecca; Tamminga, Caleb; Shi, Zhe; Borchardt, Christian; Jambulapati, Jayaram; Bai, Ruoli; Wanniarachchi, Hashini; Bueno, Lorena; Hamel,Ernest; Mason, Ralph P; Trawick, Mary Lynn; Pinney, Kevin G
  3. Bioorganic & Medicinal Chemistry. 2024, Nov 07; 118: 117981.
  1. 3.   Structural basis for cell type specific DNA binding of C/EBPß: the case of cell cycle inhibitor p15INK4b promoter
  2. Lountos, George T; Cherry, Scott; Tropea, Joseph E; Wlodawer, Alexander; Miller, Maria
  3. Journal of Structural Biology. 2022, Nov 04; 214(4): 107918.
  1. 4.   Design, Synthesis and Biological Investigation of 2-Anilino Triazolopyrimidines as Tubulin Polymerization Inhibitors with Anticancer Activities
  2. Romagnoli, Romeo; Oliva, Paola; Prencipe, Filippo; Manfredini, Stefano; Budassi, Federica; Brancale, Andrea; Ferla, Salvatore; Hamel,Ernest; Corallo, Diana; Aveic, Sanja; Manfreda, Lorenzo; Mariotto, Elena; Bortolozzi, Roberta; Viola, Giampietro
  3. Pharmaceuticals (Basel, Switzerland). 2022, Aug 21; 15(8):
  1. 5.   Identification of a CD4-binding site-directed antibody with ADCC activity from a chronic HIV-1B'-infected Chinese donor
  2. Hu, Yuanyuan; Li, Dan; Fu, Hongyang; Hao, Yanling; Ren, Li; Wang, Shuo; Hu,Xintao; Shao, Yiming; Hong, Kunxue; Wang, Zheng
  3. Virus research. 2021, Sep; 302: 198470.
  1. 6.   Identification and Structure of a Multidonor Class of Head-Directed Influenza-Neutralizing Antibodies Reveal the Mechanism for Its Recurrent Elicitation
  2. Cheung, Crystal Sao-Fong; Fruehwirth, Alexander; Paparoditis, Philipp Carl Georg; Shen, Chen-Hsiang; Foglierini, Mathilde; Joyce, M Gordon; Leung, Kwanyee; Piccoli, Luca; Rawi, Reda; Silacci-Fregni, Chiara; Tsybovsky,Yaroslav; Verardi, Raffaello; Wang, Lingshu; Wang, Shuishu; Yang, Eun Sung; Zhang, Baoshan; Zhang, Yi; Chuang, Gwo-Yu; Corti, Davide; Mascola, John R; Shapiro, Lawrence; Kwong, Peter D; Lanzavecchia, Antonio; Zhou, Tongqing
  3. Cell reports. 2020, Sep 01; 32(9): 108088.
  1. 7.   Design, synthesis, in vitro and in vivo biological evaluation of 2-amino-3-aroylbenzo[b]furan derivatives as highly potent tubulin polymerization inhibitors
  2. Oliva, Paola; Romagnoli, Romeo; Manfredini, Stefano; Brancale, Andrea; Ferla, Salvatore; Hamel,Ernest; Ronca, Roberto; Maccarinelli, Federica; Giacomini, Arianna; Rruga, Fatlum; Mariotto, Elena; Viola, Giampietro; Bortolozzi, Roberta
  3. European journal of medicinal chemistry. 2020, AUG 15; 200: 112448.
  1. 8.   Low-level alternative tRNA priming of reverse transcription of HIV-1 and SIV in vivo
  2. Fennessey,Christine; Camus, Celine; Immonen,Taina; Reid,Carolyn; Maldarelli,Frank; Lifson,Jeffrey; Keele,Brandon
  3. Retrovirology. 2019, Apr 4; 16(1):
  1. 9.   Glycan Masking Focuses Immune Responses to the HIV-1 CD4-Binding Site and Enhances Elicitation of VRC01-Class Precursor Antibodies
  2. Duan, Hongying; Chen, Xuejun; Boyington, Jeffrey C; Cheng, Cheng; Zhang, Yi; Jafari, Alexander J; Stephens, Tyler; Tsybovsky, Yaroslav; Kalyuzhniy, Oleksandr; Zhao, Peng; Menis, Sergey; Nason, Martha C; Normandin, Erica; Mukhamedova, Maryam; DeKosky, Brandon J; Wells, Lance; Schief, William R; Tian, Ming; Alt, Frederick W; Kwong, Peter D; Mascola, John R
  3. Immunity. 2018, Aug 21; 49(2): 301-311.e5.
  1. 10.   Quantification of the Impact of the HIV-1-Glycan Shield on Antibody Elicitation
  2. Zhou, Tongqing; Doria-Rose, Nicole A; Cheng, Cheng; Stewart-Jones, Guillaume B E; Chuang, Gwo-Yu; Chambers, Michael; Druz, Aliaksandr; Geng, Hui; McKee, Krisha; Kwon, Young Do; O'Dell, Sijy; Sastry, Mallika; Schmidt, Stephen D; Xu, Kai; Chen, Lei; Chen, Rita E; Louder, Mark K; Pancera, Marie; Wanninger, Timothy G; Zhang, Baoshan; Zheng, Anqi; Farney, S Katie; Foulds, Kathryn E; Georgiev, Ivelin S; Joyce, M Gordon; Lemmin, Thomas; Narpala, Sandeep; Rawi, Reda; Soto, Cinque; Todd, John-Paul; Shen, Chen-Hsiang; Tsybovsky, Yaroslav; Yang, Yongping; Zhao, Peng; Haynes, Barton F; Stamatatos, Leonidas; Tiemeyer, Michael; Wells, Lance; Scorpio, Diana G; Shapiro, Lawrence; McDermott, Adrian B; Mascola, John R; Kwong, Peter D
  3. Cell Reports. 2017, Apr 25; 19(4): 719-732.
  1. 11.   Crystal structures of beta-1,4-galactosyltransferase 7 enzyme reveal conformational changes and substrate binding
  2. Tsutsui, Y.; Ramakrishnan, B.; Qasba, P. K.
  3. Journal of Biological Chemistry. 2013, 1-Nov; 288(44): 31963-70.
  1. 12.   Synthesis and Antitumor Molecular Mechanism of Agents Based on Amino 2-(3 ',4 ',5 '-Trimethoxybenzoyl)benzo[b]furan: Inhibition of Tubulin and Induction of Apoptosis
  2. Romagnoli, R.; Baraldi, P. G.; Lopez-Cara, C.; Cruz-Lopez, O.; Carrion, M. D.; Salvador, M. K.; Bermejo, J.; Estevez, S.; Estevez, F.; Balzarini, J.; Brancale, A.; Ricci, A.; Chen, L. C.; Kim, J. G.; Hamel, E.
  3. Chemmedchem. 2011, Oct; 6(10): 1841-1853.
  1. 13.   Conformational and Structural Features of HIV-1 gp120 Underlying the Dual Receptor Antagonism by Cross-Reactive Neutralizing Antibody m18
  2. Gift, S. K.; Zentner, I. J.; Schon, A.; McFadden, K.; Umashankara, M.; Rajagopal, S.; Contarino, M.; Duffy, C.; Courter, J. R.; Zhang, M. Y.; Gershoni, J. M.; Cocklin, S.; Dimitrov, D. S.; Smith, A. B.; Freire, E.; Chaiken, I. M.
  3. Biochemistry. 2011, Apr; 50(14): 2756-2768.
  1. 14.   Polymorphism in Alzheimer A beta Amyloid Organization Reflects Conformational Selection in a Rugged Energy Landscape
  2. Miller, Y.; Ma, B.; Nussinov, R.
  3. Chemical Reviews. 2010, Aug; 110(8): 4820-4838.
  1. 15.   Lysine120 Interactions with p53 Response Elements can Allosterically Direct p53 Organization
  2. Pan, Y. P.; Nussinov, R.
  3. Plos Computational Biology. 2010, Aug; 6(8): e1000878.
  1. 16.   Zinc ions promote Alzheimer A beta aggregation via population shift of polymorphic states
  2. Miller, Y.; Ma, B. Y.; Nussinov, R.
  3. Proceedings of the National Academy of Sciences of the United States of America. 2010, May 25; 107(21): 9490-9495.
  1. 17.   Allosteric activation of E2-RING finger-mediated ubiquitylation by a structurally defined specific E2-binding region of gp78
  2. Das, R.; Mariano, J.; Tsai, Y. C.; Kalathur, R. C.; Kostova, Z.; Li, J.; Tarasov, S. G.; McFeeters, R. L.; Altieri, A. S.; Ji, X.; Byrd, R. A.; Weissman, A. M.
  3. Molecular Cell. 2009, Jun 26; 34(6): 674-85.
  1. 18.   Cooperativity Dominates the Genomic Organization of p53-Response Elements: A Mechanistic View
  2. Pan, Y. P.; Nussinov, R.
  3. Plos Computational Biology. 2009 5(7):
  1. 19.   Discovery of novel tumor suppressor p53 response elements using information theory
  2. Lyakhov, I. G.; Krishnamachari, A.; Schneider, T. D.
  3. Nucleic Acids Research. 2008 36(11): 3828-3833.
  1. 20.   Structural definition of a conserved neutralization epitope on HIV-1 gp120
  2. Zhou, T. Q.; Xu, L.; Dey, B.; Hessell, A. J.; Van Ryk, D.; Xiang, S. H.; Yang, X. Z.; Zhang, M. Y.; Zwick, M. B.; Arthos, J.; Burton, D. R.; Dimitrov, D. S.; Sodroski, J.; Wyatt, R.; Nabel, G. J.; Kwong, P. D.
  3. Nature. 2007, Feb; 445(7129): 732-737.
  1. 21.   Anatomy of Escherichia coli sigma(70) promoters
  2. Shultzaberger, R. K.; Chen, Z. H.; Lewis, Janine; Schneider, Tom
  3. Nucleic Acids Research. 2007, Feb; 35(3): 771-788.
  1. 22.   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. 23.   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. 24.   Association of putative concave protein-binding sites with the fluctuation behavior of residues
  2. Ertekin, A.; Nussinov, R.; Haliloglu, T.
  3. Protein Science. 2006, Oct; 15(10): 2265-2277.
  1. 25.   Homology model of RSK2 N-terminal kinase domain, structure-based identification of novel RSK2 inhibitors, and preliminary common pharmacophore
  2. Nguyen, T. L.; Gussio, R.; Smith, J. A.; Lannigan, D. A.; Hecht, S. M.; Scudiero, D. A.; Shoemaker, R. H.; Zaharevitz, D. W.
  3. Bioorganic & Medicinal Chemistry. 2006, Sep; 14(17): 6097-6105.
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