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  1. 1.   Evolution of Thyroglobulin Loop Kinetics in EpCAM
  2. Chen, Serena H.; Bell,David
  3. LIFE-BASEL. 2021, Sep 03; 11(9):
  1. 2.   A terminal alpha 3-galactose modification regulates an E3 ubiquitin ligase subunit in Toxoplasma gondii
  2. Mandalasi, Msano; Kim, Hyun W.; Thieker, David; Sheikh, M. Osman; Gas-Pascual, Elisabet; Rahman,Kazi; Zhao, Peng; Daniel, Nitin G.; van der Wel, Hanke; Ichikawa, H. Travis; Glushka, John N.; Wells, Lance; Woods, Robert J.; Wood, Zachary A.; West, Christopher M.
  3. JOURNAL OF BIOLOGICAL CHEMISTRY. 2020, JUL 3; 295(27): 9223-9243.
  1. 3.   Molecular dynamics based improvement of the solubilizing self-cleavable tag Zbasic-?I-CM application in the preparation of recombinant proteins in Escherichia coli
  2. Luo, Han; Hu, Lifu; Ma,Buyong; Zhao, Meiqi; Luo, Manyu; Deng, Qing; Deng, Shaorong; Ye, Hao; Lin, Tong; Chen, Junsheng; Wang, Tao; Zhu, Jianwei; Lu, Huili
  3. Biochemical and biophysical research communications. 2019, MAY 28; 513(2): 412-418.
  1. 4.   Raf-1 Cysteine-Rich Domain Increases the Affinity of K-Ras/Raf at the Membrane, Promoting MAPK Signaling
  2. Li, Shuai; Jang, Hyunbum; Zhang, Jian; Nussinov, Ruth
  3. Structure . 2018, Mar 6; 26(3): 513-+.
  1. 5.   Familial Mutations May Switch Conformational Preferences in alpha-Synuclein Fibrils
  2. Xu, Liang; Ma, Buyong; Nussinov, Ruth; Thompson, Damien
  3. ACS CHEMICAL NEUROSCIENCE. 2017, Apr 19; 8(4):
  1. 6.   Protocols for Molecular Dynamics Simulations of RNA Nanostructures.
  2. Kim, Taejin; Kasprzak, Wojciech; Shapiro, Bruce
  3. Methods in molecular biology (Clifton, N.J.). 2017 1632: 33-64.
  1. 7.   Amylin-Abeta oligomers at atomic resolution using molecular dynamics simulations: a link between Type 2 diabetes and Alzheimer's disease
  2. Baram, M.; Atsmon-Raz, Y.; Ma, B.; Nussinov, R.; Miller, Y.
  3. Physical chemistry chemical physics : PCCP. 2016, 28-Jan; 18(4): 2330-8.
  1. 8.   Dynamic conformational changes in the rhesus TRIM5alpha dimer dictate the potency of HIV-1 restriction
  2. Lamichhane, R.; Mukherjee, S.; Smolin, N.; Pauszek, R. F., 3rd; Bradley, M.; Sastri, J.; Robia, S. L.; Millar, D.; Campbell, E. M.
  3. Virology. 2016, Jan; 500: 161-168.
  1. 9.   Symmetry-Based Self-assembled Nanotubes Constructed Using Native Protein Structures: The Key Role of Flexible Linkers
  2. Buch, I.; Tsai, C. J.; Wolfson, H. J.; Nussinov, R.
  3. Protein and Peptide Letters. 2011, Apr; 18(4): 362-372.
  1. 10.   Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase
  2. Seibold, S. A.; Singh, B. N.; Zhang, C. F.; Kireeva, M.; Domecq, C.; Bouchard, A.; Nazione, A. M.; Feig, M.; Cukier, R. I.; Coulombe, B.; Kashlev, M.; Hampsey, M.; Burton, Z. F.
  3. Biochimica Et Biophysica Acta-Gene Regulatory Mechanisms. 2010, Aug; 1799(8): 575-587.
  1. 11.   Synthesis and conformational analysis of locked carbocyclic analogues of 1,3-diazepinone riboside, a high-affinity cytidine deaminase inhibitor
  2. Ludek, O. R.; Schroeder, G. K.; Liao, C.; Russ, P. L.; Wolfenden, R.; Marquez, V. E.
  3. Journal of Organic Chemistry. 2009, Aug 21; 74(16): 6212-23.
  1. 12.   Understanding antibody-antigen associations by molecular dynamics simulations: Detection of important intra- and inter-molecular salt bridges
  2. Sinha, N.; Li, Y. L.; Lipschultz, C. A.; Smith-Gill, S. J.
  3. Cell Biochemistry and Biophysics. 2007 47(3): 361-375.
  1. 13.   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. 14.   A common pharmacophore for a diverse set of colchicine site inhibitors using a structure-based approach
  2. Nguyen, T. L.; McGrath, C.; Hermone, A. R.; Burnett, J. C.; Zaharevitz, D. W.; Day, B. W.; Wipf, P.; Hamel, E.; Gussio, R.
  3. Journal of Medicinal Chemistry. 2005, SEP 22; 48(19): 6107-6116.
  1. 15.   Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: Significant role of Asn ladder
  2. Tsai, H. H.; Reches, M.; Tsai, C. J.; Gunasekaran, K.; Gazit, E.; Nussinov, R.
  3. Proceedings of the National Academy of Sciences of the United States of America. 2005, JUN 7; 102(23): 8174-8179.
  1. 16.   Binding affinity difference induced by the stereochemistry of the sulfoxide bridge of the cyclic peptide inhibitors of Grb2-SH2 domain: NMR studies for the structural origin
  2. Shi, Y. H.; Song, Y. L.; Lin, D. H.; Tan, J. Z.; Roller, P. P.; Li, Q.; Long, Y. Q.; Song, G. Q.
  3. Biochemical and Biophysical Research Communications. 2005, MAY 20; 330(4): 1254-1261.
  1. 17.   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. 18.   Comparison of the protein-protein interfaces in the p53-DNA crystal structures: Towards elucidation of the biological interface
  2. Ma, B. Y.; Pan, Y. P.; Gunasekaran, K.; Venkataraghavan, R. B.; Levine, A. J.; Nussinov, R.
  3. Proceedings of the National Academy of Sciences of the United States of America. 2005, MAR 15; 102(11): 3988-3993.
  1. 19.   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. 20.   A comparative study of amyloid fibril formation by residues 15-19 of the human calcitonin hormone: A single beta-sheet model with a small hydrophobic core
  2. Haspel, N.; Zanuy, D.; Ma, B. Y.; Wolfson, H.; Nussinov, R.
  3. Journal of Molecular Biology. 2005, FEB 4; 345(5): 1213-1227.
  1. 21.   Release factors eRF1 and RF2 - A universal mechanism controls the large conformational changes
  2. Ma, B. Y.; Nussinov, R.
  3. Journal of Biological Chemistry. 2004, DEC 17; 279(51): 53875-53885.
  1. 22.   Structure-based discovery of nonpeptidic small organic compounds to block the T cell response to myelin basic protein
  2. Koehler, N. K. U.; Yang, C. Y.; Varady, J.; Lu, Y. P.; Wu, X. W.; Liu, M.; Yin, D. X.; Bartels, M.; Xu, B. Y.; Roller, P. P.; Long, Y. Q.; Li, P.; Kattah, M.; Cohn, M. L.; Moran, K.; Tilley, E.; Richert, J. R.; Wang, S. M.
  3. Journal of Medicinal Chemistry. 2004, OCT 7; 47(21): 4989-4997.
  1. 23.   In silico protein design by combinatorial assembly of protein building blocks
  2. Tsai, H. H.; Tsai, C. J.; Ma, B. Y.; Nussinov, R.
  3. Protein Science. 2004, OCT; 13(10): 2753-2765.
  1. 24.   Molecular dynamics simulation of E-coli dihydrofolate reductase and its circular permuted variants: Relative stabilities in experiment and simulations
  2. Hu, Z. J.; Ma, B. Y.; Nussinov, R.; Southerl, W. M.
  3. Abstracts of Papers of the American Chemical Society. 2004, AUG 22; 228(Part 1): 123-COMP, Abstract U519-123-COMP, Abstract U519.
  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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