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  1. 1.   Defining the Landscape of the Pauling-Corey Rippled Sheet: An Orphaned Motif Finding New Homes
  2. Raskatov, Jevgenij A.; Schneider,Joel; Nilsson, Bradley L.
  3. Accounts of chemical research. 2021, MAY 18; 54: 2488-2501.
  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.   Fast and accurate modeling of protein-protein interactions by combining template-interface-based docking with flexible refinement
  2. Tuncbag, N.; Keskin, O.; Nussinov, R.; Gursoy, A.
  3. Proteins-Structure Function and Bioinformatics. 2012, Apr; 80(4): 1239-1249.
  1. 4.   Fiber Dock: Flexible induced-fit backbone refinement in molecular docking
  2. Mashiach, E.; Nussinov, R.; Wolfson, H. J.
  3. Proteins-Structure Function and Bioinformatics. 2010, May; 78(6): 1503-1519.
  1. 5.   FireDock: a web server for fast interaction refinement in molecular docking
  2. Mashiach, E.; Schneidman-Duhovny, D.; Andrusier, N.; Nussinov, R.; Wolfson, H. J.
  3. Nucleic Acids Research. 2008 36: W229-W232.
  1. 6.   Mining the NCI antiviral compounds for HIV-1 integrase inhibitors
  2. Deng, J. X.; Kelley, J. A.; Barchi, J. J.; Sanchez, T.; Dayam, R.; Pommier, Y.; Neamati, N.
  3. Bioorganic & Medicinal Chemistry. 2006, JUN 1; 14(11): 3785-3792.
  1. 7.   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. 8.   Human P2Y(6) receptor: Molecular modeling leads to the rational design of a novel agonist based on a unique conformational preference
  2. Costanzi, S.; Joshi, B. V.; Maddileti, S.; Mamedova, L.; Gonzalez-Moa, M. J.; Marquez, V. E.; Harden, T. K.; Jacobson, K. A.
  3. Journal of Medicinal Chemistry. 2005, DEC 29; 48(26): 8108-8111.
  1. 9.   Crystal structures for HIV-1 reverse transcriptase in complexes with three pyridinone derivatives: A new class of non-nucleoside inhibitors effective against a broad range of drug-resistant strains
  2. Himmel, D. M.; Das, K.; Clark, A. D.; Hughes, S. H.; Benjahad, A.; Oumouch, S.; Guillemont, J.; Coupa, S.; Poncelet, A.; Csoka, I.; Meyer, C.; Andries, K.; Nguyen, C. H.; Grierson, D. S.; Arnold, E.
  3. Journal of Medicinal Chemistry. 2005, DEC 1; 48(24): 7582-7591.
  1. 10.   Autophosphorylation of Archaeoglobus fulgidus Rio2 and crystal structures of its nucleotide-metal ion complexes
  2. Laronde-Leblanc, N.; Guszczynski, T.; Copeland, T.; Wlodawer, A.
  3. Febs Journal. 2005, JUN; 272(11): 2800-2810.
  1. 11.   Structural basis for the function of stringent starvation protein A as a transcription factor
  2. Hansen, A. M.; Gu, Y. J.; Li, M.; Andrykovitch, M.; Waugh, D. S.; Jin, D. J.; Ji, X. H.
  3. Journal of Biological Chemistry. 2005, APR 29; 280(17): 17380-17391.
  1. 12.   Dynamic behavior of the telomerase RNA hairpin structure and its relationship to dyskeratosis congenita
  2. Yingling, Y. G.; Shapiro, B. A.
  3. Journal of Molecular Biology. 2005, APR 22; 348(1): 27-42.
  1. 13.   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. 14.   In the quest for stable rescuing mutants of p53: Computational mutagenesis of flexible loop L1
  2. Pan, Y. P.; Ma, B. Y.; Venkataraghavan, R. B.; Levine, A. J.; Nussinov, R.
  3. Biochemistry. 2005, FEB 8; 44(5): 1423-1432.
  1. 15.   Discovery of protein substructures in EM maps
  2. Lasker, K.; Dror, O.; Nussinov, R.; Wolfson, H.
  3. Algorithms in bioinformatics. 2005; 3692 : 423-434.
  1. 16.   Substrate-induced conformational changes in glycosyltransferases
  2. Qasba, P. K.; Ramakrishnan, B.; Boeggeman, E.
  3. Trends in Biochemical Sciences. 2005, JAN; 30(1): 53-62.
  1. 17.   Effect of the Met344His mutation on the conformational dynamics of bovine beta-1,4-galactosyltransferase: Crystal structure of the Met344His mutant in complex with chitobiose
  2. Ramakrishnan, B.; Boeggeman, E.; Qasba, P. K.
  3. Biochemistry. 2004, OCT 5; 43(39): 12513-12522.
  1. 18.   Structure and catalytic cycle of beta-1,4-galactosyltransferase
  2. Ramakrishnan, B.; Boeggeman, E.; Ramasamy, V.; Qasba, P. K.
  3. Current Opinion in Structural Biology. 2004, OCT; 14(5): 593-600.
  1. 19.   Solution structure of the pseudo-5 ' splice site of a retroviral splicing suppressor
  2. Cabello-Villegas, J.; Giles, K. E.; Soto, A. M.; Yu, P.; Mougin, A.; Beemon, K. L.; Wang, Y. X.
  3. Rna-a Publication of the Rna Society. 2004, SEP; 10(9): 1388-1398.
  1. 20.   Mechanism of the guanosine triphosphate hydrolysis by RAS-GAP proteins as studied by the flexible effective fragment QM/MM technique
  2. Grigorenko, B.; Nemukhin, A.; Topol, I. A.; Cachau, R. E.; Burt, S. K.
  3. Abstracts of Papers of the American Chemical Society. 2004, AUG 22; 228(638-PHYS, Part 2): U295-U295.
  1. 21.   Applications of the flexible effective fragment QM/MM technique for modeling biomolecular processes
  2. Nemukhin, A.; Grigorenko, B.; Topol, I. A.; Burt, S. K.
  3. Abstracts of Papers of the American Chemical Society. 2004, AUG 22; 228(269-PHYS, Part 2): U240-U241.
  1. 22.   Conformationally constrained diacylglycerol (DAG) analogs: 4-C-hydroxyethyl-5-O-acyl-2,3-dideoxy-D-glyceropentono-1,4-lactone analogs as protein kinase C (PKC) ligands
  2. Lee, J.; Kim, S. Y.; Kang, J. H.; Acs, G.; Acs, P.; Blumberg, P. M.; Marquez, V. E.
  3. European Journal of Medicinal Chemistry. 2004 39(1): 69-77.
  1. 23.   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. 24.   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. 25.   Modulating functional loop movements: The role of highly conserved residues in the correlated loop motions
  2. Gunasekaran, K.; Nussinov, R.
  3. Chembiochem. 2004 5(2): 224-230.
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