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  1. 1.   A practical guide to large-scale docking
  2. Bender, Brian J.; Gahbauer, Stefan; Luttens, Andreas; Lyu, Jiankun; Webb, Chase M.; Stein, Reed M.; Fink, Elissa A.; Balius,Trent; Carlsson, Jens; Irwin, John J.; Shoichet, Brian K.
  3. Nature protocols. 2021, Oct; 16(10): 4799-4832.
  1. 2.   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. 3.   RNA-DNA fibers and polygons with controlled immunorecognition activate RNAi, FRET and transcriptional regulation of NF-B in human cells
  2. Ke, Weina; Hong, Enping; Saito, Renata F.; Rangel, Maria Cristina; Wang, Jian; Viard,Mathias; Richardson, Melina; Khisamutdinov, Emil F.; Panigaj, Martin; Dokholyan, Nikolay; Chammas, Roger; Dobrovolskaia, Marina A.; Afonin, Kirill A.
  3. Nucleic acids research. 2019, FEB 20; 47(3): 1350-1361.
  1. 4.   PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps (vol 72, pg 1137, 2016)
  2. Kuzu, Guray; Keskin, Ozlem; Nussinov, Ruth; Gursoy, Attila
  3. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY. 2018, JAN; 74(Pt 1): 65-66.
  1. 5.   PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps
  2. Kuzu, G.; Keskin, O.; Nussinov, R.; Gursoy, A.
  3. Acta crystallographica. Section D, Structural biology. 2016, 1-Oct; 72(Pt 10): 1137-1148.
  1. 6.   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. 7.   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. 8.   A Boost for the Emerging Field of RNA Nanotechnology Report on the First International conference on RNA Nanotechnology
  2. Shukla, G. C.; Hague, F.; Tor, Y.; Wilhelmsson, L. M.; Toulme, J. J.; Isambert, H.; Guo, P. X.; Rossi, J. J.; Tenenbaum, S. A.; Shapiro, B. A.
  3. Acs Nano. 2011, May; 5(5): 3405-3418.
  1. 9.   Coarse-graining RNA nanostructures for molecular dynamics simulations
  2. Paliy, M.; Melnik, R.; Shapiro, B. A.
  3. Physical Biology. 2010, Sep; 7(3): 12.
  1. 10.   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. 11.   Architecture and secondary structure of an entire HIV-1 RNA genome
  2. Watts, J. M.; Dang, K. K.; Gorelick, R. J.; Leonard, C. W.; Bess, J. W.; Swanstrom, R.; Burch, C. L.; Weeks, K. M.
  3. Nature. 2009 460(7256): 711-U87.
  1. 12.   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. 13.   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. 14.   RNA secondary structure prediction from sequence alignments using a network of k-nearest neighbor classifiers
  2. Bindewald, E.; Shapiro, B. A.
  3. Rna-a Publication of the Rna Society. 2006 12(3): 342-352.
  1. 15.   Combinatorial docking approach for structure prediction of large proteins and multi-molecular assemblies
  2. Inbar, Y.; Benyamini, H.; Nussinov, R.; Wolfson, H. J.
  3. Physical Biology. 2005, DEC; 2(4, Sp. Iss.): S156-S165.
  1. 16.   Computational intelligence, bioinformatics and computational biology: A brief overview of methods, problems and perspectives
  2. Kasabov, N.; Sidorov, I. A.; Dimitrov, D. S.
  3. Journal of Computational and Theoretical Nanoscience. 2005, DEC; 2(4): 473-491.
  1. 17.   From structure to function: Methods and applications
  2. Wolfson, H. J.; Shatsky, M.; Schneidman-Duhovny, D.; Dror, O.; Shulman-Peleg, A.; Ma, B. Y.; Nussinov, R.
  3. Current Protein & Peptide Science. 2005, APR; 6(2): 171-183.
  1. 18.   Multiple docking for protein structure prediction
  2. Inbar, Y.; Wolfson, H. J.; Nussinov, R.
  3. International Journal of Robotics Research. 2005, FEB-MAR; 24(2-3): 131-150.
  1. 19.   Structural polymorphism of the HIV-1 leader region explored by computational methods
  2. Kasprzak, W.; Bindewald, E.; Shapiro, B. A.
  3. Nucleic Acids Research. 2005 33(22): 7151-7163.
  1. 20.   A model of the ACE2 structure and function as a SARS-CoV receptor
  2. Prabakaran, P.; Mao, X. D.; Dimitrov, D. S.
  3. Biochemical and Biophysical Research Communications. 2004 314(1): 235-241.
  1. 21.   Reducing the computational complexity of protein folding via fragment folding and assembly
  2. Haspel, N.; Tsai, C. J.; Wolfson, H.; Nussinov, R.
  3. Protein Science. 2003 12(6): 1177-1187.
  1. 22.   Hierarchical protein folding pathways: A computational study of protein fragments
  2. Haspel, N.; Tsai, C. J.; Wolfson, H.; Nussinov, R.
  3. Proteins-Structure Function and Genetics. 2003 51(2): 203-215.
  1. 23.   The palm subdomain-based active site is internally permuted in viral RNA-dependent RNA polymerases of an ancient lineage
  2. Gorbalenya, A. E.; Pringle, F. M.; Zeddam, J. L.; Luke, B. T.; Cameron, C. E.; Kalmakoff, J.; Hanzlik, T. N.; Gordon, K. H. J.; Ward, V. K.
  3. Journal of Molecular Biology. 2002 324(1): 47-62.
  1. 24.   Stem Trace: An interactive visual tool for comparative RNA structure analysis
  2. Kasprzak, W.; Shapiro, B. A.
  3. Bioinformatics. 1999 15(1): 16-31.
  1. 25.   Distinguishing between sequential and nonsequentially folded proteins: Implications for folding and misfolding
  2. Tsai, C. J.; Maizel, J. V.; Nussinov, R.
  3. Protein Science. 1999 8(8): 1591-1604.
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