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  1. 1.   NMR 1H, 13C, and 15N resonance assignments of the oncogenic Q61R variant of human NRAS in the active, GTP-bound conformation
  2. Sharma,Alok; Tonelli, Marco; Dyba,Marcin; Esposito,Dominic; Esposito,Dominic; Nissley,Dwight; McCormick, Frank; Maciag,Anna
  3. Biomolecular NMR Assignments. 2025, May 02;
  1. 2.   Predicting RNA SHAPE scores with deep learning
  2. Bliss, Noah; Bindewald,Eckart; Shapiro,Bruce
  3. RNA biology. 2020, JUN 1; 1-7.
  1. 3.   Modeling ligand docking to RNA in the design of RNA-based nanostructures
  2. Kasprzak,Wojciech; Ahmed, Nour Ali; Shapiro,Bruce
  3. Current opinion in biotechnology. 2020, JUN; 63: 16-25.
  1. 4.   Structure of E3 ligase E6AP with a proteasome-binding site provided by substrate receptor hRpn10
  2. Buel,Gwen; Chen,Xiang; Chari,Raj; O'Neill, Maura J; Ebelle, Danielle L; Jenkins, Conor; Sridharan, Vinidhra; Tarasov,Sergey; Tarasova,Nadya; Andresson,Thorkell; Walters,Kylie
  3. Nature communications. 2020, Mar 10; 11(1): 1291.
  1. 5.   Conformational Switch to a beta-Turn in a Staphylococcal Quorum Sensing Signal Peptide Causes a Dramatic Increase in Potency
  2. Vasquez, Joseph K.; West, Korbin H. J.; Yang, Tian; Polaske, Thomas J.; Cornilescu,Gabriel; Tonelli, Marco; Blackwell, Helen E.
  3. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 2020, JAN 15; 142(2): 750-761.
  1. 6.   Probing the Structures of Viral RNA Regulatory Elements with SHAPE and Related Methodologies
  2. Rausch, Jason; Sztuba-Solinska, Joanna; Legrice, Stuart
  3. Frontiers in Microbiology. 2018, Jan 9; 8: 2634.
  1. 7.   Probing Structural Features of Alzheimer's Amyloid-beta Pores in Bilayers Using Site-Specific Amino Acid Substitutions
  2. Capone, R.; Jang, H.; Kotler, S. A.; Kagan, B. L.; Nussinov, R.; Lal, R.
  3. Biochemistry. 2012, Jan; 51(3): 776-785.
  1. 8.   Multistrand RNA Secondary Structure Prediction and Nanostructure Design Including Pseudoknots
  2. Bindewald, E.; Afonin, K.; Jaeger, L.; Shapiro, B. A.
  3. Acs Nano. 2011, Dec; 5(12): 9542-9551.
  1. 9.   Femtomole SHAPE Reveals Regulatory Structures in the Authentic XMRV RNA Genome
  2. Grohman, J. K.; Kottegoda, S.; Gorelick, R. J.; Allbritton, N. L.; Weeks, K. M.
  3. Journal of the American Chemical Society. 2011, Dec; 133(50): 20326-20334.
  1. 10.   Correlating SHAPE signatures with three-dimensional RNA structures
  2. Bindewald, E.; Wendeler, M.; Legiewicz, M.; Bona, M. K.; Wang, Y.; Pritt, M. J.; Le Grice, S. F. J.; Shapiro, B. A.
  3. Rna-a Publication of the Rna Society. 2011, Sep; 17(9): 1688-1696.
  1. 11.   RNA Folding in Transcription Elongation Complex IMPLICATION FOR TRANSCRIPTION TERMINATION
  2. Lubkowska, L.; Maharjan, A. S.; Komissarova, N.
  3. Journal of Biological Chemistry. 2011, Sep; 286(36): 31576-31585.
  1. 12.   Polymorphic Triple beta-Sheet Structures Contribute to Amide Hydrogen/Deuterium (H/D) Exchange Protection in the Alzheimer Amyloid beta 42 Peptide
  2. Ma, B. Y.; Nussinov, R.
  3. Journal of Biological Chemistry. 2011, Sep; 286(39): 34244-34253.
  1. 13.   SHAPE analysis of the FIV Leader RNA reveals a structural switch potentially controlling viral packaging and genome dimerization
  2. Kenyon, J. C.; Tanner, S. J.; Legiewicz, M.; Phillip, P. S.; Rizvi, T. A.; Le Grice, S. F. J.; Lever, A. M. L.
  3. Nucleic Acids Research. 2011, Aug; 39(15): 6692-6704.
  1. 14.   Protein structure prediction using a docking-based hierarchical folding scheme
  2. Kifer, I.; Nussinov, R.; Wolfson, H. J.
  3. Proteins-Structure Function and Bioinformatics. 2011, Jun; 79(6): 1759-1773.
  1. 15.   Initiation complex dynamics direct the transitions between distinct phases of early HIV reverse transcription
  2. Liu, S. X.; Harada, B. T.; Miller, J. T.; Le Grice, S. F. J.; Zhuang, X. W.
  3. Nature Structural & Molecular Biology. 2010, Dec; 17(12): 1453-U83.
  1. 16.   The RNA Transport Element of the Murine musD Retrotransposon Requires Long-range Intramolecular Interactions for Function
  2. Legiewicz, M.; Zolotukhin, A. S.; Pilkington, G. R.; Purzycka, K. J.; Mitchell, M.; Uranishi, H.; Bear, J.; Pavlakis, G. N.; Le Grice, S. F. J.; Felber, B. K.
  3. Journal of Biological Chemistry. 2010, Dec; 285(53): 42097-42104.
  1. 17.   Iterative Structure-Based Peptide-Like Inhibitor Design against the Botulinum Neurotoxin Serotype A
  2. Zuniga, J. E.; Hammill, J. T.; Drory, O.; Nuss, J. E.; Burnett, J. C.; Gussio, R.; Wipf, P.; Bavari, S.; Brunger, A. T.
  3. Plos One. 2010, Jun; 5(6): 15.
  1. 18.   Computer Simulations of Peptides from the p53 DNA Binding Domain
  2. Khalili, M.; Wales, D. J.
  3. Journal of Chemical Theory and Computation. 2009 5(5): 1380-1392.
  1. 19.   Determination of Multicomponent Protein Structures in Solution Using Global Orientation and Shape Restraints
  2. Wang, J. B.; Zuo, X. B.; Yu, P.; Byeon, I.; Jung, J. W.; Wang, X. X.; Dyba, M.; Seifert, S.; Schwieters, C. D.; Qin, J.; Gronenborn, A. M.; Wang, Y. X.
  3. Journal of the American Chemical Society. 2009 131(30): 10507-10515.
  1. 20.   Computational strategies for the automated design of RNA nanoscale structures from building blocks using NanoTiler
  2. Bindewald, E.; Grunewald, C.; Boyle, B.; O'Connor, M.; Shapiro, B. A.
  3. Journal of Molecular Graphics & Modelling. 2008 27(3): 299-308.
  1. 22.   Constructing templates for protein structure prediction by simulation of protein folding pathways
  2. Kifer, I.; Nussinov, R.; Wolfson, H. J.
  3. Proteins-Structure Function and Bioinformatics. 2008 73(2): 380-394.
  1. 23.   RNA-binding protein HuR interacts with thrombomodulin 5 ' untranslated region and represses internal ribosome entry site-mediated translation under IL-1 beta treatment
  2. Yeh, C. H.; Hung, L. Y.; Hsu, C.; Le, S. Y.; Lee, P. T.; Liao, W. L.; Lin, Y. T.; Chang, W. C.; Tseng, J. T.
  3. Molecular Biology of the Cell. 2008 19(9): 3812-3822.
  1. 24.   Data mining of imperfect double-stranded RNA in 3 ' untranslated regions of eukaryotic mRNAs
  2. Le, S. Y.; Maizel, J. V.
  3. Biomolecular Engineering. 2007, Sep; 24(3): 351-359.
  1. 25.   Vif is a RNA chaperone that could temporally regulate RNA dimerization and the early steps of HIV-1 reverse transcription
  2. Henriet, S.; Sinck, L.; Bec, G.; Gorelick, R. J.; Marquet, R.; Paillart, J. C.
  3. Nucleic Acids Research. 2007, Aug; 35(15): 5141-5153.
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