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simone's library [176 articles]

最近录入 simone's 文献库.
  • Multiscale modeling of nucleic acids: Insights into DNA flexibility
    Biopolymers, Vol. 89, No. 9. (2008), pp. 722-731.
    by Yannick J Bomble, David A Case
    posted to dna by simone on 2008-09-04 20:37:33 as ** along with 1 person onufriev
  • A Unification of the Elastic Network Model and the Gaussian Network Model for Optimal Description of Protein Conformational Motions and Fluctuations
    Biophys. J., Vol. 94, No. 10. (15 May 2008), pp. 3853-3857.
    by Wenjun Zheng
    posted to enm by simone on 2008-09-04 20:34:24 as ** along with 1 person aqeel
  • A molecular dynamics simulation study of an aminoglycoside/A-site RNA complex: conformational and hydration patterns.
    Biochimie, Vol. 88, No. 8. (August 2006), pp. 1061-1073.
    by AC Vaiana, E Westhof, P Auffinger
    posted to rna by simone on 2008-09-01 14:21:20 as **
  • Water and ion binding around RNA and DNA (C,G) oligomers.
    J Mol Biol, Vol. 300, No. 5. (28 July 2000), pp. 1113-1131.
    by P Auffinger, E Westhof
    posted to rna by simone on 2008-08-31 21:45:34 as ** along with 3 people and 1 group lillekatt ffranca sobolevnrm baker-group
  • Docking of aminoglycosides to hydrated and flexible RNA.
    Journal of medicinal chemistry, Vol. 49, No. 3. (9 February 2006), pp. 1023-1033.
    by N Moitessier, E Westhof, S Hanessian
    posted to rna by simone on 2008-08-31 21:25:55 as **
  • On secondary structure rearrangements and equilibria of small RNAs.
    Chembiochem : a European journal of chemical biology, Vol. 4, No. 10. (6 October 2003), pp. 984-990.
    by R Micura, C Höbartner
    posted to rna by simone on 2008-08-31 17:13:21 as **
  • A 1.3-A resolution crystal structure of the HIV-1 trans-activation response region RNA stem reveals a metal ion-dependent bulge conformation.
    Proc Natl Acad Sci U S A, Vol. 95, No. 17. (18 August 1998), pp. 9819-9824.
    by JA Ippolito, TA Steitz
    posted to rna by simone on 2008-08-31 16:58:58 as ** along with 1 person lillekatt
  • Recognition of double-stranded RNA by proteins and small molecules
    Biopolymers, Vol. 70, No. 1. (2003), pp. 86-102.
    by Coby B Carlson, Olen M Stephens, Peter A Beal
    posted to rna by simone on 2008-08-31 14:59:40 as **
  • Sequence and structure space of RNA-binding peptides
    Biopolymers, Vol. 70, No. 1. (2003), pp. 80-85.
    by Chandreyee Das, Alan D Frankel
    posted to rna by simone on 2008-08-31 14:59:15 as **
  • Chemical and functional diversity of small molecule ligands for RNA.
    Biopolymers, Vol. 70, No. 1. (September 2003), pp. 4-18.
    by T Hermann
    posted to rna by simone on 2008-08-29 15:55:13 as **
  • The linkage between magnesium binding and RNA folding.
    Journal of molecular biology, Vol. 317, No. 4. (5 April 2002), pp. 507-521.
    by VK Misra, DE Draper
    posted to rna by simone on 2008-08-27 23:40:27 as **
  • Aminoglycoside binding to the hammerhead ribozyme: a general model for the interaction of cationic antibiotics with RNA.
    Journal of molecular biology, Vol. 276, No. 5. (13 March 1998), pp. 903-912.
    by T Hermann, E Westhof
    posted to rna by simone on 2008-08-27 23:32:40 as **
  • Folding intermediates of a self-splicing RNA: mispairing of the catalytic core.
    Journal of molecular biology, Vol. 280, No. 4. (24 July 1998), pp. 597-609.
    by J Pan, SA Woodson
    posted to rna by simone on 2008-08-27 16:19:34 as ** along with 1 person austin
  • Exploring the folding landscape of a structured RNA.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 1. (8 January 2002), pp. 155-160.
    by R Russell, X Zhuang, HP Babcock, IS Millett, S Doniach, S Chu, D Herschlag
    posted to rna by simone on 2008-08-27 16:15:02 as **
  • In vitro selection and characterization of RNAs with high affinity to antibiotics.
    Methods in enzymology, Vol. 318 (2000), pp. 214-229.
    by ST Wallace, R Schroeder
    posted to rna by simone on 2008-08-27 16:03:37 as **
  • Anion binding to nucleic acids.
    Structure (London, England : 1993), Vol. 12, No. 3. (March 2004), pp. 379-388.
    by P Auffinger, L Bielecki, E Westhof
    posted to rna by simone on 2008-08-26 19:52:21 as **
  • NMR and MD studies of the temperature-dependent dynamics of RNA YNMG-tetraloops.
    Nucleic acids research, Vol. 36, No. 6. (April 2008), pp. 1928-1940.
    by J Ferner, A Villa, E Duchardt, E Widjajakusuma, J Wöhnert, G Stock, H Schwalbe
    posted to rna by simone on 2008-08-26 16:51:20 as **
  • Time-resolved NMR studies of RNA folding
    Biopolymers, Vol. 86, No. 5-6. (2007), pp. 360-383.
    by Boris Fürtig, Janina Buck, Vijayalaxmi Manoharan, Wolfgang Bermel, Andres Jäschke, Philipp Wenter, Stefan Pitsch, Harald Schwalbe
    posted to rna by simone on 2008-08-26 16:35:27 as **
  • NMR studies of RNA dynamics and structural plasticity using NMR residual dipolar couplings.
    Biopolymers, Vol. 86, No. 5-6. (5 2007), pp. 384-402.
    by M Getz, X Sun, A Casiano-Negroni, Q Zhang, HM Al-Hashimi
    posted to rna by simone on 2008-08-26 16:32:09 as **
  • RNA dynamics: it is about time
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Hashim M Al-Hashimi, Nils G Walter
    posted to rna by simone on 2008-08-26 16:26:21 as ** along with 2 people ruvido barry
  • Rational ligand design for RNA: the role of static structure and conformational flexibility in target recognition.
    Biochimie, Vol. 84, No. 9. (September 2002), pp. 869-875.
    by T Hermann
    posted to rna by simone on 2008-08-26 13:46:46 as **
  • The macrolide-ketolide antibiotic binding site is formed by structures in domains II and V of 23S ribosomal RNA.
    Molecular microbiology, Vol. 31, No. 2. (January 1999), pp. 623-631.
    by LH Hansen, P Mauvais, S Douthwaite
    posted to ribosome by simone on 2008-08-22 19:35:58 as **
  • Knowledge-based design of bimodular and trimodular polyketide synthases based on domain and module swaps: a route to simple statin analogues
    Chemistry & Biology, Vol. 6, No. 10. (October 1999), pp. 731-741.
    by Anand Ranganathan, Máire Timoney, Matthew Bycroft, Jesús Cortés, Iain P Thomas, Barrie Wilkinson, Laurenz Kellenberger, Ulf Hanefeld, Ian S Galloway, James Staunton, Peter F Leadlay
    posted to rbosome by simone on 2008-08-22 19:20:20 as **
  • Engineering a polyketide with a longer chain by insertion of an extra module into the erythromycin-producing polyketide synthase.
    Chemistry & biology, Vol. 8, No. 5. (May 2001), pp. 475-485.
    by CJ Rowe, IU Böhm, IP Thomas, B Wilkinson, BA Rudd, G Foster, AP Blackaby, PJ Sidebottom, Y Roddis, AD Buss, J Staunton, PF Leadlay
    posted to ribosome by simone on 2008-08-22 19:19:51 as **
  • Chain Dynamics of Nascent Polypeptides Emerging from the Ribosome
    ACS Chem. Biol. (22 August 2008)
    by Jamie P Ellis, Courtney K Bakke, Robert N Kirchdoerfer, Lisa M Jungbauer, Silvia Cavagnero
    posted to ribosome by simone on 2008-08-22 18:43:26 as **
  • Validation of an empirical RNA-ligand scoring function for fast flexible docking using RiboDock®
    Journal of Computer-Aided Molecular Design, Vol. 18, No. 3. (March 2004), pp. 189-208.
    by David D Morley, Mohammad Afshar
    posted to docking by simone on 2008-07-21 14:28:33 as ** along with 1 person P2324548
  • Current topics in RNA-protein recognition: control of specificity and biological function through induced fit and conformational capture.
    Biochemistry, Vol. 40, No. 27. (10 July 2001), pp. 7947-7956.
    by N Leulliot, G Varani
    posted to rna by simone on 2008-07-16 16:35:12 as **
  • Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
    Journal of Computational Chemistry, Vol. 19, No. 14. (6 January 1999), pp. 1639-1662.
    by Garrett M Morris, David S Goodsell, Robert S Halliday, Ruth Huey, William E Hart, Richard K Belew, Arthur J Olson
    posted to docking by simone on 2008-07-16 14:09:42 as ** along with 13 people and 1 group dgruiz nachtalp P2324548 yongzhao peprovy tovrstra papatonyhill schlauchi carlescorbi middledomain LamBras andreramme UVA_mag_res TSRI_MGL
  • PRODRG: a tool for high-throughput crystallography of protein–ligand complexes
    Acta Crystallographica Section D: Biological Crystallography, Vol. 60, No. 8. (01 August 2004), pp. 1355-1363.
    by Schüttelkopf, , Van Aalten,
    posted to prdrg by simone on 2008-07-16 14:01:53 as ** along with 1 person dgruiz
  • Visualizing spatially correlated dynamics that directs RNA conformational transitions
    Nature, Vol. 450, No. 7173., pp. 1263-1267.
    by Qi Zhang, Andrew C Stelzer, Charles K Fisher, Hashim M Al-Hashimi
    posted to zhang by simone on 2008-07-15 16:41:54 as ** along with 7 people and 3 groups cactus sobolevnrm niallhaslam joseph_x_zhou kintoki kluck nigham baker-group HIV_DR Soft Matter
  • Docking to RNA via Root-Mean-Square-Deviation-Driven Energy Minimization with Flexible Ligands and Flexible Targets
    J. Chem. Inf. Model. (30 May 2008)
    by Christophe Guilbert, Thomas L James
    posted to rna by simone on 2008-07-15 16:34:45 as ** along with 1 person reyez
  • Binding of neomycin to the TAR element of HIV-1 RNA induces dissociation of Tat protein by an allosteric mechanism.
    Biochemistry, Vol. 37, No. 16. (21 April 1998), pp. 5549-5557.
    by S Wang, PW Huber, M Cui, AW Czarnik, HY Mei
    posted to tar-rna by simone on 2008-07-15 16:19:42 as ** along with 1 person lillekatt
  • Signal sequence-independent membrane targeting of ribosomes containing short nascent peptides within the exit tunnel.
    Nature structural & molecular biology (6 April 2008)
    by Thomas Bornemann, Johannes Jöckel, Marina V V Rodnina, Wolfgang Wintermeyer
    posted to ribsome by simone on 2008-06-13 16:06:11 as **
  • A structure-based strategy to identify new molecular scaffolds targeting the bacterial ribosomal A-site.
    Bioorg Med Chem, Vol. 12, No. 5. (1 March 2004), pp. 935-947.
    by N Foloppe, IJ Chen, B Davis, A Hold, D Morley, R Howes
    posted to ribosome by simone on 2008-06-13 15:57:12 as ** along with 1 person P2324548
  • The structures of antibiotics bound to the E site region of the 50 S ribosomal subunit of Haloarcula marismortui: 13-deoxytedanolide and girodazole.
    Journal of molecular biology, Vol. 367, No. 5. (13 April 2007), pp. 1471-1479.
    by SJ Schroeder, G Blaha, J Tirado-Rives, TA Steitz, PB Moore
    posted to ribsome by simone on 2008-06-13 11:38:05 as **
  • Interplay of signal recognition particle and trigger factor at L23 near the nascent chain exit site on the Escherichia coli ribosome.
    The Journal of cell biology, Vol. 161, No. 4. (26 May 2003), pp. 679-684.
    by RS Ullers, EN Houben, A Raine, CM ten Hagen-Jongman, M Ehrenberg, J Brunner, B Oudega, N Harms, J Luirink
    posted to l23 by simone on 2008-06-10 11:52:01 as **
  • The signal recognition particle binds to protein L23 at the peptide exit of the Escherichia coli ribosome.
    RNA (New York, N.Y.), Vol. 9, No. 5. (May 2003), pp. 566-573.
    by SQ Gu, F Peske, HJ Wieden, MV Rodnina, W Wintermeyer
    posted to l23 by simone on 2008-06-10 11:51:35 as **
  • Trigger factor binds to ribosome-signal-recognition particle (SRP) complexes and is excluded by binding of the SRP receptor.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 101, No. 21. (25 May 2004), pp. 7902-7906.
    by I Buskiewicz, E Deuerling, SQ Gu, J Jöckel, MV Rodnina, B Bukau, W Wintermeyer
    posted to ribosome by simone on 2008-06-10 11:50:31 as **
  • New Features of the Ribosome and Ribosomal Inhibitors: Non-Enzymatic Recycling, Misreading and Back-Translocation.
    Journal of molecular biology (2 May 2008)
    by Witold Szaflarski, Oliver Vesper, Yoshika Teraoka, Beata Plitta, Daniel N N Wilson, Knud H H Nierhaus
    posted to ribsome by simone on 2008-06-10 11:48:53 as **
  • Structure of trigger factor binding domain in biologically homologous complex with eubacterial ribosome reveals its chaperone action.
    Proc Natl Acad Sci U S A (9 August 2005)
    by David Baram, Erez Pyetan, Assa Sittner, Tamar Auerbach-Nevo, Anat Bashan, Ada Yonath
    posted to ribosome by simone on 2008-05-26 10:43:31 as ** along with 1 person and 1 group pdelosri EPFL_SB_ITP_LBS
  • Following translation by single ribosomes one codon at a time
    Nature (09 March 2008)
    by Jin-Der Wen, Laura Lancaster, Courtney Hodges, Ana-Carolina Zeri, Shige H Yoshimura, Harry F Noller, Carlos Bustamante, Ignacio Tinoco
    posted to ribosome by simone on 2008-05-22 16:01:10 as ** along with 4 people dchughes jonathanjacobs melting cactus
  • A structural understanding of the dynamic ribosome machine
    Nature Reviews Molecular Cell Biology, Vol. 9, No. 3., pp. 242-253.
    by Thomas A Steitz
    posted to steitz by simone on 2008-03-26 14:43:13 as ** along with 1 person zwang
  • Structural Insight Into Functional Aspects of Ribosomal RNA Targeting
    ChemBioChem, Vol. 4, No. 10. (26 September 2003), pp. 1008-1017.
    by Ada Yonath, Prof
    posted to ribosome by simone on 2008-03-26 14:34:43 as ** along with 1 person P2324548
  • Dynamics of trigger factor interaction with translating ribosomes.
    J Biol Chem, Vol. 283, No. 7. (15 February 2008), pp. 4124-4132.
    by A Rutkowska, MP Mayer, A Hoffmann, F Merz, B Zachmann-Brand, C Schaffitzel, N Ban, E Deuerling, B Bukau
    posted to ribosome by simone on 2008-03-26 14:32:48 as **
  • A peptide deformylase–ribosome complex reveals mechanism of nascent chain processing
    Nature (20 February 2008)
    by Rouven Bingel-Erlenmeyer, Rebecca Kohler, Günter Kramer, Arzu Sandikci, Snježana Antolić, Timm Maier, Christiane Schaffitzel, Brigitte Wiedmann, Bernd Bukau, Nenad Ban
    posted to ribosome by simone on 2008-03-26 14:32:30 as ** along with 1 person Evangelia
  • The antibiotic kasugamycin mimics mRNA nucleotides to destabilize tRNA binding and inhibit canonical translation initiation
    Nature Structural & Molecular Biology, Vol. 13, No. 10. (24 September 2006), pp. 871-878.
    by Frank Schluenzen, Chie Takemoto, Daniel N Wilson, Tatsuya Kaminishi, Joerg M Harms, Kyoko Hanawa-Suetsugu, Witold Szaflarski, Masahito Kawazoe, Mikako Shirouzo, Knud H Nierhaus, Shigeyuki Yokoyama, Paola Fucini
    posted to ribosome_drugs by simone on 2008-02-06 12:32:28 as ** along with 2 people dayjm namtonthat
  • Inhibition of peptide bond formation by pleuromutilins: the structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with tiamulin
    Molecular Microbiology, Vol. 54, No. 5. (2004), pp. 1287-1294.
    by Frank Schlunzen, Erez Pyetan, Paola Fucini, Ada Yonath, Jorg M Harms
    posted to ribosome_drugs by simone on 2008-02-06 12:25:18 as **
  • 23S rRNA base pair 2057-2611 determines ketolide susceptibility and fitness cost of the macrolide resistance mutation 2058A-->G.
    Proc Natl Acad Sci U S A, Vol. 102, No. 14. (5 April 2005), pp. 5180-5185.
    by P Pfister, N Corti, S Hobbie, C Bruell, R Zarivach, A Yonath, EC Böttger
    posted to ribosome_drugs by simone on 2008-02-06 10:50:59 as **
  • 23S rRNA 2058A-->G alteration mediates ketolide resistance in combination with deletion in L22.
    Antimicrob Agents Chemother, Vol. 50, No. 11. (November 2006), pp. 3816-3823.
    by R Berisio, N Corti, P Pfister, A Yonath, EC Böttger
    posted to ribosome_drugs by simone on 2008-02-06 10:15:31 as **
  • Structure-based drug design meets the ribosome
    Biochemical Pharmacology, Vol. 71, No. 7. (30 March 2006), pp. 1016-1025.
    by Francois Franceschi, Erin M Duffy
    posted to ribosome by simone on 2008-02-04 17:00:30 as **
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