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  1. 1.   Increased Single-Spectrum Top-Down Protein Sequence Coverage in Trapping Mass Spectrometers with Chimeric Ion Loading
  2. Weisbrod, Chad R.; Anderson, Lissa C.; Greer, Joseph B.; Dehart,Caroline; Hendrickson, Christopher L.
  3. ANALYTICAL CHEMISTRY. 2020, SEP 15; 92(18): 12193-12200.
  1. 2.   Non-B DB: a database of predicted non-B DNA-forming motifs in mammalian genomes
  2. Cer, R. Z.; Bruce, K. H.; Mudunuri, U. S.; Yi, M.; Volfovsky, N.; Luke, B. T.; Bacolla, A.; Collins, J. R.; Stephens, R. M.
  3. Nucleic Acids Research. 2011, Jan; 39: D383-D391.
  1. 3.   Automatic prediction of protein interactions with large scale motion
  2. Schneidman-Duhovny, D.; Nussinov, R.; Wolfson, H. J.
  3. Proteins-Structure Function and Bioinformatics. 2007, Dec; 69(4): 764-773.
  1. 4.   FireDock: Fast interaction refinement in molecular docking
  2. Andrusier, N.; Nussinov, R.; Wolfson, H. J.
  3. Proteins-Structure Function and Bioinformatics. 2007, Oct; 69(1): 139-159.
  1. 5.   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. 6.   Consensus features in amyloid fibrils: sheet-sheet recognition via a (polar or nonpolar) zipper structure
  2. Zheng, J.; Ma, B. Y.; Nussinov, R.
  3. Physical Biology. 2006, Sep; 3(3): P1-P4.
  1. 7.   Structural mimicry of CD4 by a cross-reactive HIV-1 neutralizing antibody with CDR-H2 and H3 containing unique motifs
  2. Prabakaran, P.; Gan, J. H.; Wu, Y. Q.; Zhang, M. Y.; Dimitrov, D. S.; Ji, X. H.
  3. Journal of Molecular Biology. 2006, MAR 17; 357(1): 82-99.
  1. 8.   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. 9.   Structural and dynamical classification of RNA single-base bulges for nanostructure design
  2. Hastings, W. A.; Yingling, Y. G.; Chirikjian, G. S.; Shapiro, B. A.
  3. Journal of Computational and Theoretical Nanoscience. 2006, FEB; 3(1): 63-77.
  1. 10.   Long homopurine center dot homopyrimidine sequences are characteristic of genes expressed in brain and the pseudoautosomal region
  2. Bacolla, A.; Collins, J. R.; Gold, B.; Chuzhanova, N.; Yi, M.; Stephens, R. M.; Stefanov, S.; Olsh, A.; Jakupciak, J. P.; Dean, M.; Lempicki, R. A.; Cooper, D. N.; Wells, R. D.
  3. Nucleic Acids Research. 2006 34(9): 2663-2675.
  1. 11.   Gateway vectors for the production of combinatorially-tagged His(6)-MBP fusion proteins in the cytoplasm and periplasm of Escherichia Coli
  2. Nallamsetty, S.; Austin, B. P.; Penrose, K. J.; Waugh, D. S.
  3. Protein Science. 2005, DEC; 14(12): 2964-2971.
  1. 12.   Understanding how the herpes thymidine kinase orchestrates optimal sugar and nucleobase conformations to accommodate its substrate at the active site: A chemical approach
  2. Marquez, V. E.; Choi, Y.; Comin, M. J.; Russ, P.; George, C.; Huleihel, M.; Ben-Kasus, T.; Agbaria, R.
  3. Journal of the American Chemical Society. 2005, NOV 2; 127(43): 15145-15150.
  1. 13.   Dolastatin 11 conformations, analogues and pharmacophore
  2. Ali, M. A.; Bates, R. B.; Crane, Z. D.; Dicus, C. W.; Gramme, M. R.; Hamel, E.; Marcischak, J.; Martinez, D. S.; McClure, K. J.; Nakkiew, P.; Pettit, G. R.; Stessman, C. C.; Sufi, B. A.; Yarick, G. V.
  3. Bioorganic & Medicinal Chemistry. 2005, JUL 1; 13(13): 4138-4152.
  1. 14.   Is the critical role of loop 3 of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase in catalysis due to loop-3 residues arginine-84 and tryptophan-89? Site-directed mutagenesis, biochemical, and crystallographic studies
  2. Li, Y.; Blaszczyk, J.; Wu, Y.; Shi, G. B.; Ji, X. H.; Yan, H. G.
  3. Biochemistry. 2005, JUN 21; 44(24): 8590-8599.
  1. 15.   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. 16.   Crystallography and the design of anti-AIDS drugs: Conformational flexibility and positional adaptability are important in the design of non-nucleoside HIV-1 reverse transcriptase inhibitors
  2. Das, K.; Lewi, P. J.; Hughes, S. H.; Arnold, E.
  3. Progress in Biophysics and Molecular Biology. 2005, JUN; 88(2): 209-231.
  1. 17.   PROSIT, an online service to calculate pseudorotational parameters of nucleosides and nucleotides
  2. Sun, G. Y.; Voigt, J. H.; Marquez, V. E.; Nicklaus, M. C.
  3. Nucleosides Nucleotides & Nucleic Acids. 2005 24(5-7, Sp. Iss.): 1029-1032.
  1. 18.   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. 19.   Evaluation of macrocyclic Grb2 SH2 domain-binding peptide mimetics prepared by ring-closing metathesis of C-terminal allylglycines with an N-terminal beta-vinyl-substituted phosphotyrosyl mimetic
  2. Oishi, S.; Karki, R. G.; Shi, Z. D.; Worthy, K. M.; Bindu, L.; Chertov, O.; Esposito, D.; Frank, P.; Gillette, W. K.; Maderia, M.; Hartley, J.; Nicklaus, M. C.; Barchi, J. J.; Fisher, R. J.; Burke, T. R.
  3. Bioorganic & Medicinal Chemistry. 2005 13(7): 2431-2438.
  1. 20.   Three-dimensional model of the pore form of anthrax protective antigen. Structure and biological implications
  2. Nguyen, T. L.
  3. Journal of Biomolecular Structure & Dynamics. 2004, DEC; 22(3): 253-265.
  1. 21.   Kinetic stability and crystal structure of the viral capsid protein SHP
  2. Forrer, P.; Chang, C. S.; Ott, D.; Wlodawer, A.; Pluckthun, A.
  3. Journal of Molecular Biology. 2004, NOV 12; 344(1): 179-193.
  1. 22.   Insights into amyloid structural formation and assembly through computational approaches
  2. Zanuy, D.; Gunasekaran, K.; Ma, B. Y.; Tsai, H. H.; Tsai, C. J.; Nussinov, R.
  3. Amyloid-Journal of Protein Folding Disorders. 2004, SEP; 11(3): 143-161.
  1. 23.   Characterization of unbound conformations of gp120 core domain
  2. Pan, Y. P.; Ma, B.; Nussinov, R.
  3. Abstracts of Papers of the American Chemical Society. 2004, AUG 22; 228(Part 1): 177-COMP, Abstract U527-177-COMP, Abstract U527.
  1. 24.   Roles of conformational and positional adaptability in structure-based design of TMC125-R165335 (etravirine) and related non-nucleoside reverse transcriptase inhibitors that are highly potent and effective against wild-type and drug-resistant HIV-1 variants
  2. Das, K.; Clark, A. D.; Lewi, P. J.; Heeres, J.; de Jonge, M. R.; Koymans, L. M. H.; Vinkers, H. M.; Daeyaert, F.; Ludovici, D. W.; Kukla, M. J.; De Corte, B.; Kavash, R. W.; Ho, C. Y.; Ye, H.; Lichtenstein, M. A.; Andries, K.; Pauwels, R.; de Bethune, M. P.; Boyer, P. L.; Clark, P.; Hughes, S. H.; Janssen, P. A. J.; Arnold, E.
  3. Journal of Medicinal Chemistry. 2004 47(10): 2550-2560.
  1. 25.   QM/MM modeling of the glutathione-hydroxymethyl radical reaction in watery
  2. Nemukhin, A. V.; Grigorenko, B. L.; Topol, I. A.; Burt, S. K.
  3. Physical Chemistry Chemical Physics. 2004 6(5): 1031-1038.
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