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  1. 1.   Optimization of the PROTAC linker region of the proteasome substrate receptor hRpn13 rationalized structural modeling with molecular dynamics
  2. Lu,Xiuxiu; Sabbasani, Venkata R; Walters,Kylie; Swenson, Rolf E; Walters,Kylie
  3. The Journal of Biological Chemistry. 2025, Apr 18; 108520.
  1. 2.   HIV-1 Transcription Inhibition Using Small RNA-Binding Molecules
  2. Khatkar, Pooja; Mensah, Gifty; Ning, Shangbo; Cowen, Maria; Kim, Yuriy; Williams, Anastasia; Abulwerdi, Fardokht A; Zhao, Yunjie; Zeng, Chen; Le Grice, Stuart F J; Kashanchi, Fatah
  3. Pharmaceuticals (Basel, Switzerland). 2023, Dec 25; 17(1):
  1. 3.   Novel MAPK/AKT-impairing germline NRAS variant identified in a melanoma-prone family
  2. Brown, Kevin M; Xu, Mai; Sargen, Michael; Jang,Hyunbum; Zhang,Mingzhen; Zhang, Tongwu; Zhu, Bin; Jones, Kristie; Kim, Jung; Mendoza, Laura; Hayward, Nicholas K; Tucker, Margaret A; Goldstein, Alisa M; Yang, Xiaohong Rose; Stewart, Douglas R; Hicks, Belynda; Consonni, Dario; Pesatori, Angela C; Fargnoli, Maria Concetta; Peris, Ketty; Stratigos, Alex; Menin, Chiara; Ghiorzo, Paola; Puig, Susana; Nagore, Eduardo; Andresson,Thorkell; Nussinov,Ruth; Calista, Donato; Landi, Maria Teresa
  3. Familial cancer. 2021, Jul 03;
  1. 4.   Synthesis and biological evaluation of a series of 2-(((5-akly/aryl-1H-pyrazol-3-yl)methyl)thio)-5-alkyl-6-(cyclohexylmethyl)-pyrimidin-4(3H)-ones as potential HIV-1 inhibitors
  2. Wu, Yumeng; Tang, Chengrun; Rui, Ruomei; Yang, Liumeng; Ding, Wei; Wang, Jiangyuan; Li, Yiming; Lai,Christopher; Wang, Yueping; Luo, Ronghua; Xiao, Weilie; Zhang, Hongbing; Zheng, Yongtang; He, Yanping
  3. Acta pharmaceutica Sinica. B. 2020, Mar; 10(3): 512-528.
  1. 5.   Conformational dynamics of the TTD-PHD histone reader module of the UHRF1 epigenetic regulator reveals multiple histone-binding states, allosteric regulation, and druggability
  2. Houliston, R Scott; Lemak, Alexander; Iqbal, Aman; Ivanochko, Danton; Duan, Shili; Kaustov, Lilia; Ong, Michelle S; Fan, Lixin; Senisterra, Guillermo; Brown, Peter J; Wang, Yun-Xing; Arrowsmith, Cheryl H
  3. Journal of Biological Chemistry. 2017, Dec 22; 292(51): 20947-20959.
  1. 6.   Conformational energy range of ligands in protein crystal structures: The difficult quest for accurate understanding
  2. Peach, Megan; Cachau, Raul; Nicklaus, Marc
  3. JOURNAL OF MOLECULAR RECOGNITION. 2017, Aug; 30(8):
  1. 7.   Stereoselective binding of chiral ligands to single nucleotide polymorphisms of the human organic cation transporter-1 determined using cellular membrane affinity chromatography
  2. Moaddel, R.; Bighi, F.; Yamaguchi, R.; Patel, S.; Ravichandran, S.; Wainer, I. W.
  3. Analytical Biochemistry. 2010, Jun; 401(1): 148-153.
  1. 8.   Mechanism of the chemical step for the guanosine triphosphate (GTP) hydrolysis catalyzed by elongation factor Tu
  2. Grigorenko, B. L.; Shadrina, M. S.; Topol, I. A.; Collins, J. R.; Nemukhin, A. V.
  3. Biochimica Et Biophysica Acta-Proteins and Proteomics. 2008 1784(12): 1908-1917.
  1. 9.   The impact of dyskeratosis congenita mutations on the structure and dynamics of the human telomerase RNA pseudoknot domain
  2. Yingling, Y. G.; Shapiro, B. A.
  3. Journal of Biomolecular Structure & Dynamics. 2007, Feb; 24(4): 303-319.
  1. 10.   Conformation of the HIV-1 Gag protein in solution
  2. Datta, S. A. K.; Curtis, J. E.; Ratcliff, W.; Clark, P. K.; Crist, R. M.; Lebowitz, J.; Krueger, S.; Rein, A.
  3. Journal of Molecular Biology. 2007, Jan; 365(3): 812-824.
  1. 11.   New arylthioindoles: Potent inhibitors of tubulin polymerization. 2. Structure-activity relationships and molecular modeling studies
  2. De Martino, G.; Edler, M. C.; La Regina, G.; Coluccia, A.; Barbera, M. C.; Barrow, D.; Nicholson, R. I.; Chiosis, G.; Brancale, A.; Hamel, E.; Artico, M.; Silvestri, R.
  3. Journal of Medicinal Chemistry. 2006, FEB 9; 49(3): 947-954.
  1. 12.   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. 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.   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. 15.   Elucidation of thioredoxin as a molecular target for antitumor quinols
  2. Bradshaw, T. D.; Matthews, C. S.; Cookson, J.; Chew, E. H.; Shah, M.; Bailey, K.; Monks, A.; Harris, E.; Westwell, A. D.; Wells, G.; Laughton, C. A.; Stevens, M. F. G.
  3. Cancer Research. 2005, MAY 1; 65(9): 3911-3919.
  1. 16.   Mass spectrometric analysis of the HIV-1 integrase-pyridoxal 5 '-phosphate complex reveals a new binding site for a nucleotide inhibitor
  2. Williams, K. L.; Zhang, Y. J.; Shkriabai, N.; Karki, R. G.; Nicklaus, M. C.; Kotrikadze, N.; Hess, S.; Le Grice, S. F. J.; Craigie, R.; Pathak, V. K.; Kvaratskhelia, M.
  3. Journal of Biological Chemistry. 2005, MAR 4; 280(9): 7949-7955.
  1. 17.   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. 18.   Small nonphosphorylated Grb2-SH2 domain antagonists evaluated by surface resonance plasmon technology
  2. Lung, F. D. T.; Chang, C. W.; Chong, M. C.; Liou, C. C.; Li, P.; Peach, M. L.; Nicklaus, M. C.; Lou, B. S.; Roller, P. P.
  3. Peptide Science (Biopolymers). 2005 80(5): 628-635.
  1. 19.   Model of full-length HIV-1 integrase complexed with viral DNA as template for anti-HIV drug design
  2. Karki, R. G.; Tang, Y.; Burke, T. R.; Nicklaus, M. C.
  3. Journal of Computer-Aided Molecular Design. 2004, DEC; 18(12): 739-760.
  1. 20.   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. 21.   Novel small molecule inhibitors of botulinum neurotoxin A metalloprotease activity
  2. Burnett, J. C.; Schmidt, J. J.; Stafford, R. G.; Panchal, R. G.; Nguyen, T. L.; Hermone, A. R.; Vennerstrom, J. L.; McGrath, C. F.; Lane, D. J.; Sausville, E. A.; Zaharevitz, D. W.; Gussio, R.; Bavari, S.
  3. Biochemical and Biophysical Research Communications. 2003 310(1): 84-93.
  1. 22.   On the detection of multiple-binding modes of ligands to proteins, from biological, structural, and modeling data
  2. Lewis, P. J.; de Jonge, M.; Daeyaert, F.; Koymans, L.; Vinkers, M.; Heeres, J.; Janssen, P. A. J.; Arnold, E.; Das, K.; Clark, A. D.; Hughes, S. H.; Boyer, P. L.; de Bethune, M. P.; Pauwels, R.; Andries, K.; Kukla, M.; Ludovici, D.; De Corte, B.; Kavash, R.; Ho, C.
  3. Journal of Computer-Aided Molecular Design. 2003 17(2): 129-134.
  1. 23.   Insights into the binding modes of diketo acid HIV-1 integrase inhibitors-A molecular modeling study
  2. Karki, R. G.; Nicklaus, M. C.
  3. Abstracts of Papers of the American Chemical Society. 2003 225(Part 2): U179-U179.
  1. 24.   Effect of sequence polymorphism and drug resistance on two HIV- 1 Gag processing sites
  2. Feher, A.; Weber, I. T.; Bagossi, P.; Boross, P.; Mahalingam, B.; Louis, J. M.; Copeland, T. D.; Torshin, I. Y.; Harrison, R. W.; Tozser, J.
  3. European Journal of Biochemistry. 2002 269(16): 4114-4120.
  1. 25.   Molecular modeling and dynamics studies of HIV-1 kissing loop structures
  2. Pattabiraman, N.; Martinez, H. M.; Shapiro, B. A.
  3. Journal of Biomolecular Structure & Dynamics. 2002 20(3): 397-411.
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