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simones library [86 articles]

Neue Artikel in simones Bibliothek.
  • Tensegrity I. Cell structure and hierarchical systems biology
    J Cell Sci, Vol. 116, No. 7. (1 April 2003), pp. 1157-1173.
    by Donald E Ingber
    posted to rns by simone on 2008-11-04 02:13:13 as ** along with 2 people catcremona Lorette
  • Side-chain recognition and gating in the ribosome exit tunnel.
    Proceedings of the National Academy of Sciences of the United States of America (22 October 2008)
    by Paula M M Petrone, Christopher D D Snow, Del Lucent, Vijay S S Pande
    posted to ribosome by simone on 2008-11-03 21:51:36 as ** along with 1 person and 1 group barry McCammon
  • Eukaryotic ribosomal proteins lacking a eubacterial counterpart: important players in ribosomal function
    Molecular Microbiology, Vol. 59, No. 6. (March 2006), pp. 1651-1663.
    by John Dresios, Panagiotis Panopoulos, Dennis Synetos
    posted to ribosome by simone on 2008-10-28 13:48:58 as **
  • Ribosomal crystallography: initiation, peptide bond formation, and amino acid polymerization are hampered by antibiotics.
    Annual review of microbiology, Vol. 58 (2004), pp. 233-251.
    by A Yonath, A Bashan
    posted to ribosome by simone on 2008-10-28 12:56:57 as **
  • Translational regulation via L11: molecular switches on the ribosome turned on and off by thiostrepton and micrococcin.
    Molecular cell, Vol. 30, No. 1. (11 April 2008), pp. 26-38.
    by JM Harms, DN Wilson, F Schluenzen, SR Connell, T Stachelhaus, Z Zaborowska, CM Spahn, P Fucini
    posted to ribosome by simone on 2008-10-24 17:32:03 as **
  • Mutations outside the anisomycin-binding site can make ribosomes drug-resistant.
    Journal of molecular biology, Vol. 379, No. 3. (6 June 2008), pp. 505-519.
    by G Blaha, G Gürel, SJ Schroeder, PB Moore, TA Steitz
    posted to ribosome by simone on 2008-10-20 21:59:36 as **
  • The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 105, No. 36. (9 September 2008), pp. 13339-13344.
    by DN Wilson, F Schluenzen, JM Harms, AL Starosta, SR Connell, P Fucini
    posted to ribosome by simone on 2008-10-20 21:59:23 as **
  • Crystal structure of the oxazolidinone antibiotic linezolid bound to the 50S ribosomal subunit.
    Journal of medicinal chemistry, Vol. 51, No. 12. (26 June 2008), pp. 3353-3356.
    by JA Ippolito, ZF Kanyo, D Wang, FJ Franceschi, PB Moore, TA Steitz, EM Duffy
    posted to ribosome by simone on 2008-10-20 21:58:54 as **
  • Yeast Ribosomal Protein L24 Affects the Kinetics of Protein Synthesis and Ribosomal Protein L39 Improves Translational Accuracy, While Mutants Lacking Both Remain Viable
    Biochemistry, Vol. 39, No. 24. (20 June 2000), pp. 7236-7244.
    by J Dresios, IL Derkatch, SW Liebman, D Synetos
    posted to ribosome by simone on 2008-10-05 15:53:29 as **
  • RNA bulge entropies in the unbound state correlate with peptide binding strengths for HIV-1 and BIV TAR RNA because of improved conformational access.
    Nucleic Acids Res, Vol. 26, No. 22. (15 November 1998), pp. 5212-5217.
    by B Lustig, I Bahar, RL Jernigan
    posted to rna by simone on 2008-09-22 20:40:59 as ** along with 1 person baaden
  • The complex of a designer antibiotic with a model aminoacyl site of the 30S ribosomal subunit revealed by X-ray crystallography.
    Journal of the American Chemical Society, Vol. 125, No. 12. (26 March 2003), pp. 3410-3411.
    by RJ Russell, JB Murray, G Lentzen, J Haddad, S Mobashery
    posted to ribosome by simone on 2008-09-22 19:40:36 as **
  • Structure-based computational database screening, in vitro assay, and NMR assessment of compounds that target TAR RNA.
    Chem Biol, Vol. 9, No. 2. (February 2002), pp. 185-193.
    by KE Lind, Z Du, K Fujinaga, BM Peterlin, TL James
    posted to docking by simone on 2008-09-12 02:34:12 as ** along with 1 person P2324548
  • Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models
    Bioinformatics, Vol. 23, No. 13. (1 July 2007), pp. i175-184.
    by Eran Eyal, Chakra Chennubhotla, Lee-Wei Yang, Ivet Bahar
    posted to network model anistropic by simone on 2008-09-07 18:07:26 as ** along with 3 people and 1 group joseph_x_zhou aqeel jlh64 protein_Dyn
  • Anisotropic network model: systematic evaluation and a new web interface
    Bioinformatics, Vol. 22, No. 21. (1 November 2006), pp. 2619-2627.
    by Eyal, Eran, Yang, Lee-Wei, Bahar, Ivet
    posted to elasticity by simone on 2008-09-07 17:39:47 as ** along with 2 people aqeel dimka
  • Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis.
    PHYSICAL REVIEW LETTERS, Vol. 77, No. 9. (26 August 1996), pp. 1905-1908.
    by MM Tirion
    posted to nma by simone on 2008-09-06 15:23:04 as ** along with 2 people BragilMassoud pierpo
  • Dynamics of a Small Globular Protein in Terms of Low-Frequency Vibrational Modes
    PNAS, Vol. 80, No. 12. (15 June 1983), pp. 3696-3700.
    by Nobuhiro Go, Tosiyuki Noguti, Testuo Nishikawa
    posted to nma by simone on 2008-09-06 15:17:31 as ** along with 2 people aqeel saravan
  • 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
  • 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 **
  • 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
  • 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 15 people and 2 groups A_Coletta_Thesis arlam dgruiz nachtalp P2324548 yongzhao peprovy tovrstra papatonyhill schlauchi carlescorbi middledomain LamBras andreramme UVA_mag_res group 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
  • 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 **
  • 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 **
  • 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 **
  • 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
  • Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock.
    Proteins, Vol. 46, No. 1. (1 January 2002), pp. 34-40.
    by F Osterberg, GM Morris, MF Sanner, AJ Olson, DS Goodsell
    posted to docking by simone on 2008-01-24 13:15:22 as ** along with 2 people AliceWang kazemi
  • The structure of the human immunodeficiency virus type-1 TAR RNA reveals principles of RNA recognition by Tat protein.
    J Mol Biol, Vol. 253, No. 2. (20 October 1995), pp. 313-332.
    by F Aboul-ela, J Karn, G Varani
    posted to tar-rna by simone on 2007-12-14 15:33:47 as ** along with 2 people lillekatt P2324548
  • Structure of TAR RNA complexed with a Tat-TAR interaction nanomolar inhibitor that was identified by computational screening.
    Chem Biol, Vol. 9, No. 6. (June 2002), pp. 707-712.
    by Z Du, KE Lind, TL James
    posted to tar-rna by simone on 2007-12-14 15:28:01 as ** along with 2 people lillekatt P2324548
  • Molecular docking of balanol to dynamics snapshots of protein kinase A.
    Proteins (21 October 2005)
    by Chung F F Wong, Jeremy Kua, Yingkai Zhang, T P P Straatsma, J Andrew A McCammon
    posted to docking by simone on 2007-12-14 14:49:43 as ** along with 1 person and 1 group yongzhao TSRI_MGL
  • Transient Pockets on Protein Surfaces Involved in Protein-Protein Interaction
    J. Med. Chem., Vol. 50, No. 15. (26 July 2007), pp. 3457-3464.
    by S Eyrisch, V Helms
    posted to docking by simone on 2007-12-14 14:48:04 as **
  • Exploring the folding funnel of a polypeptide chain by biophysical studies on protein fragments.
    J Mol Biol, Vol. 285, No. 3. (22 January 1999), pp. 1309-1333.
    by JL Neira, AR Fersht
    posted to protein_folding by simone on 2007-11-23 08:22:17 as **
  • Dipolar relaxation and nuclear Overhauser effects in nonrigid molecules: The effect of fluctuating internuclear distances
    The Journal of Chemical Physics, Vol. 72, No. 11. (1980), pp. 6035-6043.
    by James Tropp
    posted to nmr by simone on 2007-11-13 20:00:19 as **
  • A New Method for Coarse-Grained Elastic Normal-Mode Analysis
    J. Chem. Theory Comput., Vol. 2, No. 3. (9 May 2006), pp. 464-471.
    by M Lu, B Poon, J Ma
    posted to nma by simone on 2007-11-13 19:51:00 as ** along with 2 people aqeel jlh64
  • BioMagResBank
    Nucl. Acids Res. (4 November 2007), gkm957.
    by Eldon L Ulrich, Hideo Akutsu, Jurgen F Doreleijers, Yoko Harano, Yannis E Ioannidis, Jundong Lin, Miron Livny, Steve Mading, Dimitri Maziuk, Zachary Miller, Eiichi Nakatani, Christopher F Schulte, David E Tolmie, Kent, Hongyang Yao, John L Markley
    posted to db by simone on 2007-11-07 19:07:19 as **
  • Prediction of protein conformational freedom from distance constraints.
    Proteins, Vol. 29, No. 2. (October 1997), pp. 240-251.
    by BL de Groot, DM van Aalten, RM Scheek, A Amadei, G Vriend, HJ Berendsen
    posted to first by simone on 2007-10-31 10:18:32 as **
  • Vibrational dynamics of transfer RNAs: comparison of the free and synthetase-bound forms.
    J Mol Biol, Vol. 281, No. 5. (4 September 1998), pp. 871-884.
    by I Bahar, RL Jernigan
    posted to trna by simone on 2007-10-31 09:11:34 as ** along with 2 people and 1 group joseph_x_zhou aqeel protein_Dyn
  • Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations
    Proteins: Structure, Function, and Genetics, Vol. 11, No. 3. (1991), pp. 205-217.
    by Toshiko Ichiye, Martin Karplus
    posted to pca by simone on 2007-10-11 10:22:58 as ** along with 2 people and 1 group baaden ssomani structure-bii
  • Resolving fast and slow motions in the internal loop containing stem-loop 1 of HIV-1 that are modulated by Mg2+ binding: role in the kissing-duplex structural transition.
    Nucleic Acids Res, Vol. 35, No. 5. (2007), pp. 1698-1713.
    by X Sun, Q Zhang, HM Al-Hashimi
    posted to tar by simone on 2007-10-08 10:17:57 as **
  • Structural insights into peptide bond formation
    PNAS, Vol. 99, No. 18. (3 September 2002), pp. 11670-11675.
    by Jeffrey L Hansen, Martin T Schmeing, Peter B Moore, Thomas A Steitz
    posted to ribsome by simone on 2007-07-12 09:04:35 as **
  • Erythromycin resistance by ribosome modification.
    Antimicrob Agents Chemother, Vol. 39, No. 3. (March 1995), pp. 577-585.
    by B Weisblum
    posted to antibiotica by simone on 2007-07-12 08:48:05 as **
  • Residue Specific Ribose and Nucleobase Dynamics of the cUUCGg RNA Tetraloop Motif by MNMR 13C Relaxation
    Journal of Biomolecular NMR, Vol. 32, No. 4. (August 2005), pp. 295-308.
    by Elke Duchardt, Harald Schwalbe
    posted to nmr by simone on 2006-11-06 14:43:54 as **
  • A twisted tRNA intermediate sets the threshold for decoding
    RNA, Vol. 9, No. 4. (1 April 2003), pp. 384-385.
    by Michael Yarus, Mikel Valle, Joachim Frank
    posted to rna_recognition by simone on 2006-10-17 15:58:38 as **
  • Thermodynamics of protein-peptide interactions in the ribonuclease-S system studied by molecular dynamics and free energy calculations.
    Biochemistry, Vol. 31, No. 36. (15 September 1992), pp. 8661-8674.
    by T Simonson, AT Brünger
    posted to diverses by simone on 2006-10-01 15:37:56 as **
  • Dynamic information from protein crystallography , : An analysis of temperature factors from refinement of the hen egg-white lysozyme structure
    Journal of Molecular Biology, Vol. 130, No. 3. (25 May 1979), pp. 231-253.
    by MJE Sternberg, DEP Grace, DC Phillips
    posted to x-ray by simone on 2006-10-01 14:24:58 as **
  • Changes in flexibility upon binding: Application of the self-consistent pair contact probability method to protein-protein interactions
    The Journal of Chemical Physics, Vol. 117, No. 21. (2002), pp. 9927-9933.
    by Lawrence S Canino, Tongye Shen, Andrew J Mccammon
    posted to flexibility by simone on 2006-10-01 14:20:49 as **
  • Structure of the RNA signal essential for translational frameshifting in HIV-1.
    J Mol Biol, Vol. 349, No. 5. (24 June 2005), pp. 1024-1035.
    by C Gaudin, MH Mazauric, M Traïkia, E Guittet, S Yoshizawa, D Fourmy
    posted to rna_structure by simone on 2006-08-18 10:54:50 as **
  • Structure of stem-loop IV of Tetrahymena telomerase RNA
    The EMBO Journal, Vol. aop, No. current. (06 July 2006)
    by Yu Chen, Jessica Fender, Jason D Legassie, Michael B Jarstfer, Tracy M Bryan, Gabriele Varani
    posted to rna_structure by simone on 2006-08-18 10:54:32 as **
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