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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.   Identification of Cis-Acting Elements in the 3 '-Untranslated Region of the Dengue Virus Type 2 RNA That Modulate Translation and Replication
  2. Manzano, M.; Reichert, E. D.; Polo, S.; Falgout, B.; Kasprzak, W.; Shapiro, B. A.; Padmanabhan, R.
  3. Journal of Biological Chemistry. 2011, Jun; 286(25): 22521-22534.
  1. 3.   CyloFold: secondary structure prediction including pseudoknots
  2. Bindewald, E.; Kluth, T.; Shapiro, B. A.
  3. Nucleic Acids Research. 2010, Jul; 38: W368-W372.
  1. 4.   An Intergenic Non-Coding rRNA Correlated with Expression of the rRNA and Frequency of an rRNA Single Nucleotide Polymorphism in Lung Cancer Cells
  2. Shiao, Y. H.; Lupascu, S. T.; Gu, Y. D.; Kasprzak, W.; Hwang, C. J.; Fields, J. R.; Leighty, R. M.; Quinones, O.; Shapiro, B. A.; Alvord, W. G.; Anderson, L. M.
  3. Plos One. 2009, Oct; 4(10): 11.
  1. 5.   The fraction of RNA that folds into the correct branched secondary structure determines hepatitis delta virus type 3 RNA editing levels
  2. Linnstaedt, S. D.; Kasprzak, W. K.; Shapiro, B. A.; Casey, J. L.
  3. Rna-a Publication of the Rna Society. 2009 15(6): 1177-1187.
  1. 6.   Structural domains within the 3 ' untranslated region of Turnip crinkle virus
  2. McCormack, J. C.; Yuan, X. F.; Yingling, Y. G.; Kasprzak, W.; Zamora, R. E.; Shapiro, B. A.; Simon, A. E.
  3. Journal of Virology. 2008 82(17): 8706-8720.
  1. 7.   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. 8.   Graphical exploratory data analysis of RNA secondary structure dynamics predicted by the massively parallel genetic algorithm
  2. Shapiro, B. A.; Kasprzak, W.; Grunewald, C.; Aman, J.
  3. Journal of Molecular Graphics & Modelling. 2006, Dec; 25(4): 514-531.
  1. 9.   A pseudoknot in a preactive form of a viral RNA is part of a structural switch activating minus-strand synthesis
  2. Zhang, J. C.; Zhang, G. H.; Guo, R.; Shapiro, B. A.; Simon, A. E.
  3. Journal of Virology. 2006, Sep; 80(18): 9181-9191.
  1. 10.   Structural differentiation of the HIV-1 poly(A) signals
  2. Gee, A. H.; Kasprzak, W.; Shapiro, B. A.
  3. Journal of Biomolecular Structure & Dynamics. 2006, FEB; 23(4): 417-428.
  1. 11.   A base-specific recognition signal in the 5 ' consensus sequence of rotavirus plus-strand RNAs promotes replication of the double-stranded RNA genome segments
  2. Tortorici, M. A.; Shapiro, R. A.; Patton, J. T.
  3. Rna-a Publication of the Rna Society. 2006, JAN; 12(1): 133-146.
  1. 12.   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. 13.   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. 14.   Prediction of multimolecular assemblies by multiple docking
  2. Inbar, Y.; Benyamini, H.; Nussinov, R.; Wolfson, H. J.
  3. Journal of Molecular Biology. 2005, JUN 3; 349(2): 435-447.
  1. 15.   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. 16.   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. 17.   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. 18.   Glycine N-methyltransferase tumor susceptibility gene in the benzo(a)pyrene-detoxification pathway
  2. Chen, S. Y.; Lin, J. R. V.; Darbha, R.; Lin, P. P.; Liu, T. Y.; Chen, Y. M. A.
  3. Cancer Research. 2004 64(10): 3617-3623.
  1. 19.   Predicting molecular interactions in silico: I. A guide to pharmacophore identification and its applications to drug design
  2. Dror, O.; Shulman-Peleg, A.; Nussinov, R.; Wolfson, H. J.
  3. Current Medicinal Chemistry. 2004 11(1): 71-90.
  1. 20.   Predicting molecular interactions in silico: II. Protein- protein and protein-drug docking
  2. Schneidman-Duhovny, D.; Nussinov, R.; Wolfson, H. J.
  3. Current Medicinal Chemistry. 2004 11(1): 91-107.
  1. 21.   Principles of docking: An overview of search algorithms and a guide to scoring functions
  2. Halperin, I.; Ma, B. Y.; Wolfson, H.; Nussinov, R.
  3. Proteins-Structure Function and Genetics. 2002 47(4): 409-443.
  1. 22.   RNA folding pathway functional intermediates: Their prediction and analysis
  2. Shapiro, B. A.; Bengali, D.; Kasprzak, W.; Wu, J. C.
  3. Journal of Molecular Biology. 2001 312(1): 27-44.
  1. 23.   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. 24.   Protein structure prediction in a 210-type lattice model: Parameter optimization in the genetic algorithm using orthogonal array
  2. Sun, Z. R.; Xia, X. F.; Guo, Q.; Xu, D.
  3. Journal of Protein Chemistry. 1999 18(1): 39-46.
  1. 25.   A method for biomolecular structural recognition and docking allowing conformational flexibility
  2. Sandak, B.; Nussinov, R.; Wolfson, H. J.
  3. Journal of Computational Biology. 1998 5(4): 631-654.
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