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eckart_bindewald structure [66 articles]

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  • Strategies for measuring evolutionary conservation of RNA secondary structures
    BMC Bioinformatics, Vol. 9 (26 February 2008), 122.
    by Andreas R Gruber, Stefan H Bernhart, Ivo L Hofacker, Stefan Washietl
    posted to conservation evolution rna secondary structure by eckart_bindewald on 2008-03-21 16:54:03 as *** along with 3 people and 1 group ilh stajich gresillaud Berkeley Mycology
  • Automated de novo prediction of native-like RNA tertiary structures
    PNAS (28 August 2007), 0703836104.
    by Rhiju Das, David Baker
    posted to fragment prediction rna structure by eckart_bindewald on 2007-12-06 14:36:50 as read along with 6 people and 2 groups reyez jwm marcius zwang physics Ema BioinfoCIPF SGU-CIPF
  • High-resolution structure prediction and the crystallographic phase problem
    Nature (14 October 2007)
    by Bin Qian, Srivatsan Raman, Rhiju Das, Philip Bradley, Airlie J Mccoy, Randy J Read, David Baker
    posted to ab_initio crystallography nmr prediction protein star3 structure x-ray by eckart_bindewald on 2007-11-19 12:47:07 as ***** along with 15 people and 2 groups ardalby apaydin aheilbut jwm chad_davis ffranca dgront massivemayhem cjeans zwang cactus sobolevnrm boris_aguilar Ema chenway OPIG baker-group
  • Evolutionary rates vary among rRNA structural elements
    Nucl. Acids Res., Vol. 35, No. 10. (11 May 2007), pp. 3339-3354.
    by S Smit, J Widmann, R Knight
    posted to evolution mutation prediction ribosome rna structure by eckart_bindewald on 2007-10-26 13:26:48 as *** along with 5 people and 3 groups marcius balicea penka i000 cjeans BioinfoCIPF SGU-CIPF YY1
  • Modeling RNA tertiary structure motifs by graph-grammars.
    Nucleic Acids Res, Vol. 35, No. 5. (2007), pp. 1726-1736.
    by K St-Onge, P Thibault, S Hamel, F Major
    posted to graph motif rna structure by eckart_bindewald on 2007-10-23 14:25:06 as *** along with 1 person debatebob
  • Small libraries of protein fragments model native protein structures accurately.
    J Mol Biol, Vol. 323, No. 2. (18 October 2002), pp. 297-307.
    by R Kolodny, P Koehl, L Guibas, M Levitt
    posted to assembly fragment prediction protein structure by eckart_bindewald on 2007-03-09 17:30:58 as ** along with 3 people and 2 groups ana barry j3xucite structural_bioinformatics Bioinformatics
  • Sequence-structure specificity--how does an inverse folding approach work?
    Protein Eng, Vol. 10, No. 4. (April 1997), pp. 317-331.
    by WP Hu, A Godzik, J Skolnick
    posted to assembly folding fragment inverse protein structure by eckart_bindewald on 2007-03-09 17:28:09 as **
  • On the nature of the protein folding code.
    Proc Natl Acad Sci U S A, Vol. 90, No. 2. (15 January 1993), pp. 644-648.
    by S Rackovsky
    posted to assembly fragment prediction protein structure by eckart_bindewald on 2007-03-09 17:23:49 as **
  • Predicting novel protein folds by using FRAGFOLD.
    Proteins, Vol. Suppl 5 (2001), pp. 127-132.
    by DT Jones
    posted to assembly fragment prediction protein structure by eckart_bindewald on 2007-03-09 17:15:43 as **
  • Combining local-structure, fold-recognition, and new fold methods for protein structure prediction.
    Proteins, Vol. 53 Suppl 6 (2003), pp. 491-496.
    by K Karplus, R Karchin, J Draper, J Casper, Y Mandel-Gutfreund, M Diekhans, R Hughey
    posted to fragment library prediction protein structure by eckart_bindewald on 2007-03-09 17:14:18 as ** along with 1 person j3xucite
  • Some fundamental aspects of building protein structures from fragment libraries.
    Protein Sci, Vol. 13, No. 6. (June 2004), pp. 1636-1650.
    by JB Holmes, J Tsai
    posted to fragment library prediction protein structure by eckart_bindewald on 2007-03-09 17:11:21 as ** along with 2 people and 2 groups barry wouterboomsma structural_bioinformatics Bioinformatics
  • Shaping up the protein folding funnel by local interaction: Lesson from a structure prediction study
    PNAS, Vol. 103, No. 9. (28 February 2006), pp. 3141-3146.
    by George Chikenji, Yoshimi Fujitsuka, Shoji Takada
    posted to assembly fragment prediction protein structure by eckart_bindewald on 2007-03-09 17:08:04 as ** along with 4 people wouterboomsma sotaro rsantana saunders
  • Multiple structural alignment and clustering of RNA sequences.
    Bioinformatics (25 February 2007)
    by Elfar Torarinsson, Jakob H H Havgaard, Jan Gorodkin
    posted to alignment rna secondary secondary_structure structure by eckart_bindewald on 2007-03-01 11:27:50 as *** along with 7 people and 2 groups marcius eweaver ppgardne ilh zwang dunnp zhouyu BioinfoCIPF SGU-CIPF
  • Computational RNA secondary structure design: empirical complexity and improved methods
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by Rosalia A Hernandez, Holger Hoos, Anne Condon
    posted to structure secondary rna design by eckart_bindewald on 2007-02-07 14:51:32 as **** along with 1 person and 1 group mgaldzic CHIP
  • Complete suboptimal folding of RNA and the stability of secondary structures.
    Biopolymers, Vol. 49, No. 2. (February 1999), pp. 145-165.
    by S Wuchty, W Fontana, IL Hofacker, P Schuster
    posted to structure stability secondary robustness rna canalization by eckart_bindewald on 2007-01-23 17:14:50 as read along with 3 people and 2 groups marcius arcticrasta ilh BioinfoCIPF SGU-CIPF
  • Modelling 'evo-devo' with RNA.
    Bioessays, Vol. 24, No. 12. (December 2002), pp. 1164-1177.
    by W Fontana
    posted to structure secondary robustness rna mutation genetic canalization by eckart_bindewald on 2007-01-23 16:57:41 as ***** along with 3 people rklancer evaf alexisgallagher
  • Viral RNA and evolved mutational robustness.
    J Exp Zool, Vol. 285, No. 2. (15 August 1999), pp. 119-127.
    by A Wagner, PF Stadler
    posted to structure secondary robustness rna mutation by eckart_bindewald on 2007-01-23 16:29:09 as ***** along with 1 person gokhan
  • The robustness of naturally and artificially selected nucleic acid secondary structures.
    J Mol Evol, Vol. 58, No. 6. (June 2004), pp. 681-691.
    by LA Meyers, JF Lee, M Cowperthwaite, AD Ellington
    posted to structure secondary robustness rna mutation by eckart_bindewald on 2007-01-23 16:27:10 as *****
  • Secondary structure computer prediction of the poliovirus 5' non-coding region is improved by a genetic algorithm.
    Comput Appl Biosci, Vol. 13, No. 1. (February 1997), pp. 1-12.
    by KM Currey, BA Shapiro
    posted to structure secondary robustness rna prediction persistence mutation genetic algorithm by eckart_bindewald on 2007-01-23 16:22:01 as read
  • Kinetic dissection of fundamental processes of eukaryotic translation initiation in vitro.
    EMBO J, Vol. 18, No. 23. (1 December 1999), pp. 6705-6717.
    by JR Lorsch, D Herschlag
    posted to rna secondary secondary_structure structure translation_initiation by eckart_bindewald on 2006-12-07 18:14:00 as read
  • Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.
    Genome Res, Vol. 15, No. 8. (August 2005), pp. 1034-1050.
    by A Siepel, G Bejerano, JS Pedersen, AS Hinrichs, M Hou, K Rosenbloom, H Clawson, J Spieth, LW Hillier, S Richards, GM Weinstock, RK Wilson, RA Gibbs, WJ Kent, W Miller, D Haussler
    posted to conserved noncoding prediction rna secondary structure by eckart_bindewald on 2006-09-22 19:20:36 as **** along with 14 people and 2 groups pradiptaray bpb aprasad balajis indigoviolet brant adepace djkt olympos sujaikumar Stew cisevol dmc elfar EisenLab cis-regulatory-evolution
  • Computational methods for RNA structure determination.
    Curr Opin Struct Biol, Vol. 11, No. 3. (June 2001), pp. 282-286.
    by F Major, R Griffey
    posted to prediction review rna star2 structure by eckart_bindewald on 2006-09-13 13:52:23 as read along with 3 people and 2 groups lillekatt P2324548 marcius BioinfoCIPF SGU-CIPF
  • Application of the RNA structure classification system, CSNA, to NMR structure determination.
    Nucleic Acids Res Suppl, No. 3. (2003), pp. 127-128.
    by S Baba, A Takasu, K Watanabe, G Kawai
    posted to classification ontology rna structure by eckart_bindewald on 2006-09-13 13:23:24 as *** along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
  • Novel selenoproteins identified in silico and in vivo by using a conserved RNA structural motif.
    J Biol Chem, Vol. 274, No. 53. (31 December 1999), pp. 38147-38154.
    by A Lescure, D Gautheret, P Carbon, A Krol
    posted to genome rna structure by eckart_bindewald on 2006-08-29 14:39:40 as ***
  • Computer modeling 16 S ribosomal RNA
    Journal of Molecular Biology, Vol. 221, No. 3. (5 October 1991), pp. 889-907.
    by John M Hubbard, John E Hearst
    posted to 16s 3d distance_geometry prediction structure by eckart_bindewald on 2006-08-29 14:30:29 as read along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
  • Prediction of the three-dimensional structure of Escherichia coli 30S ribosomal subunit: a molecular mechanics approach.
    Proc Natl Acad Sci U S A, Vol. 87, No. 5. (March 1990), pp. 1950-1954.
    by A Malhotra, RK Tan, SC Harvey
    posted to 30s 3d prediction ribosome structure by eckart_bindewald on 2006-08-29 14:09:32 as read
  • A dynamic programming algorithm for RNA structure prediction including pseudoknots.
    J Mol Biol, Vol. 285, No. 5. (5 February 1999), pp. 2053-2068.
    by E Rivas, SR Eddy
    posted to prediction pseudoknot rna secondary structure by eckart_bindewald on 2006-08-29 13:24:13 as **** along with 9 people and 1 group evaf balajis arcticrasta dquest condon Hosna jarasch physics guxiyou beta
  • Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction.
    BMC Bioinformatics, Vol. 5 (5 August 2004)
    by KJ Doshi, JJ Cannone, CW Cobaugh, RR Gutell
    posted to mfold prediction rna secondary structure by eckart_bindewald on 2006-08-29 12:25:21 as *** along with 1 person arcticrasta
  • A periodic pattern of mRNA secondary structure created by the genetic code
    Nucl. Acids Res., Vol. 34, No. 8. (8 May 2006), pp. 2428-2437.
    by Svetlana A Shabalina, Aleksey Y Ogurtsov, Nikolay A Spiridonov
    posted to initiation secondary star3 structure translation utr by eckart_bindewald on 2006-07-17 12:00:13 as read along with 2 people and 1 group penka raylim Nie
  • mRNAs containing extensive secondary structure in their 5' non-coding region translate efficiently in cells overexpressing initiation factor eIF-4E.
    EMBO J, Vol. 11, No. 11. (November 1992), pp. 4153-4158.
    by AE Koromilas, A Lazaris-Karatzas, N Sonenberg
    posted to initiation rna secondary structure translation utr by eckart_bindewald on 2006-06-07 13:54:03 as read
  • Insertion mutagenesis to increase secondary structure within the 5' noncoding region of a eukaryotic mRNA reduces translational efficiency.
    Cell, Vol. 40, No. 3. (March 1985), pp. 515-526.
    by J Pelletier, N Sonenberg
    posted to initiation rna secondary structure translation utr by eckart_bindewald on 2006-06-07 13:37:51 as **
  • The involvement of mRNA secondary structure in protein synthesis.
    Biochem Cell Biol, Vol. 65, No. 6. (June 1987), pp. 576-581.
    by J Pelletier, N Sonenberg
    posted to initiation rna secondary structure translation by eckart_bindewald on 2006-06-07 13:34:28 as **
  • Conserved tertiary structure elements in the 5' untranslated region of human enteroviruses and rhinoviruses.
    Virology, Vol. 191, No. 2. (December 1992), pp. 858-866.
    by SY Le, JH Chen, N Sonenberg, JV Maizel
    posted to rna secondary structure translation utr by eckart_bindewald on 2006-06-07 13:21:17 as **
  • Computational methods for the prediction of protein interactions.
    Curr Opin Struct Biol, Vol. 12, No. 3. (June 2002), pp. 368-373.
    by A Valencia, F Pazos
    posted to 3d information mutual protein structure by eckart_bindewald on 2006-03-07 20:41:59 as *** along with 1 person marti
  • Evolutionarily Conserved Pathways of Energetic Connectivity in Protein Families
    Science, Vol. 286, No. 5438. (08 October 1999), pp. 295-299.
    by Steve W Lockless, Rama Ranganathan
    posted to 3d information mutual protein structure by eckart_bindewald on 2006-03-07 20:37:57 as **** along with 15 people and 5 groups stevanspringer Einat marcius analogAI dgront caporaso sriram_s choonpeng Haggan rabio mottonen zambujo mingzhi bethbromley ca3295 structural_bioinformatics FAB-lab biomedical-nlp BioinfoCIPF SGU-CIPF
  • Evolutionarily conserved networks of residues mediate allosteric communication in proteins.
    Nat Struct Biol, Vol. 10, No. 1. (January 2003), pp. 59-69.
    by GM Süel, SW Lockless, MA Wall, R Ranganathan
    posted to 3d information mutual protein structure by eckart_bindewald on 2006-03-07 20:32:37 as *** along with 15 people and 3 groups ca3295 lna dimka marcius gbart analogAI nirfriedman dgront caporaso choonpeng efge carlescorbi mingzhi yalexeev weisblum biomedical-nlp BioinfoCIPF SGU-CIPF
  • Comparison of P-RnaPredict and mfold - algorithms for RNA secondary structure prediction.
    Bioinformatics (10 February 2006)
    by Kay C C Wiese, Andrew Hendriks
    posted to ga prediction rna secondary structure by eckart_bindewald on 2006-02-14 16:01:24 as * along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
  • Modeling the three-dimensional structure of RNA.
    FASEB J, Vol. 7, No. 1. (January 1993), pp. 97-105.
    by D Gautheret, R Cedergren
    posted to 3d distance geometry prediction rna structure tertiary by eckart_bindewald on 2006-02-07 21:58:27 as ** along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
  • HotKnots: heuristic prediction of RNA secondary structures including pseudoknots.
    RNA, Vol. 11, No. 10. (October 2005), pp. 1494-1504.
    by J Ren, B Rastegari, A Condon, HH Hoos
    posted to pseudoknot rna secondary structure by eckart_bindewald on 2006-02-06 21:35:30 as ** along with 6 people and 3 groups marcius arcticrasta condon Hosna jarasch guxiyou beta BioinfoCIPF SGU-CIPF
  • Thermodynamics of RNA-RNA Binding.
    Bioinformatics (29 January 2006)
    by Ulrike Mückstein, Hakim Tafer, Jörg Hackermüller, Stephan H H Bernhart, Peter F F Stadler, Ivo L L Hofacker
    posted to prediction rna secondary structure by eckart_bindewald on 2006-02-06 12:27:25 as **** along with 6 people and 3 groups marcius andersbj arcticrasta ilh mtw physics microRNA BioinfoCIPF SGU-CIPF
  • Statistical Inference for Well-ordered Structures in Nucleotide Sequences.
    Proc IEEE Comput Soc Bioinform Conf, Vol. 2 (2003), pp. 190-196.
    by SY Le, JH Chen, JV Maize
    posted to microrna rna secondary structure by eckart_bindewald on 2006-02-06 12:21:43 as **
  • Sequence to Structure (S2S): display, manipulate and interconnect RNA data from sequence to structure.
    Bioinformatics, Vol. 21, No. 15. (1 August 2005), pp. 3320-3321.
    by F Jossinet, E Westhof
    posted to design manipulation nanotechnology rna structure by eckart_bindewald on 2006-01-24 18:31:44 as *** along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
  • Inferring consensus structure from nucleic acid sequences.
    Comput Appl Biosci, Vol. 7, No. 3. (July 1991), pp. 347-352.
    by DK Chiu, T Kolodziejczak
    posted to information mutual prediction secondary structure trna by eckart_bindewald on 2006-01-23 21:32:38 as read
  • The complete atomic structure of the large ribosomal subunit at 2.4 A resolution.
    Science, Vol. 289, No. 5481. (11 August 2000), pp. 905-920.
    by N Ban, P Nissen, J Hansen, PB Moore, TA Steitz
    posted to 3d ribosome structure by eckart_bindewald on 2006-01-20 13:46:37 as *** along with 2 people P2324548 ruvido
  • RNA secondary structure prediction based on free energy and phylogenetic analysis.
    J Mol Biol, Vol. 289, No. 4. (18 June 1999), pp. 935-947.
    by V Juan, C Wilson
    posted to prediction rna secondary structure by eckart_bindewald on 2006-01-04 14:05:50 as read along with 1 person arcticrasta
  • Secondary structure prediction for aligned RNA sequences.
    J Mol Biol, Vol. 319, No. 5. (21 June 2002), pp. 1059-1066.
    by IL Hofacker, M Fekete, PF Stadler
    posted to alignment prediction rna secondary structure by eckart_bindewald on 2006-01-04 14:02:23 as read along with 7 people evaf balajis ppgardne arcticrasta ilh xiaobeizhao raylim
  • Crystal Structure of the Ribosome at 5.5 A Resolution
    Science, Vol. 292, No. 5518. (04 May 2001), pp. 883-896.
    by Marat M Yusupov, Gulnara Z Yusupova, Albion Baucom, Kate Lieberman, Thomas N Earnest, JHD Cate, Harry F Noller
    posted to ribosome rna secondary structure by eckart_bindewald on 2006-01-04 13:13:41 as read along with 3 people and 3 groups anita marcius equipediaz structure-bii BioinfoCIPF SGU-CIPF
  • Secondary structure model for bacterial 16S ribosomal RNA: phylogenetic, enzymatic and chemical evidence.
    Nucleic Acids Res, Vol. 8, No. 10. (24 May 1980), pp. 2275-2293.
    by CR Woese, LJ Magrum, R Gupta, RB Siegel, DA Stahl, J Kop, N Crawford, J Brosius, R Gutell, JJ Hogan, HF Noller
    posted to compensatory rna secondary sequence structure by eckart_bindewald on 2006-01-04 12:49:33 as read along with 2 people and 1 group mcox condon beta
  • The microRNAs of Caenorhabditis elegans.
    Genes Dev, Vol. 17, No. 8. (15 April 2003), pp. 991-1008.
    by LP Lim, NC Lau, EG Weinstein, A Abdelhakim, S Yekta, MW Rhoades, CB Burge, DP Bartel
    posted to microrna prediction rna secondary structure by eckart_bindewald on 2005-12-19 20:37:51 as *** along with 3 people and 1 group tardigrade mtagaya akiezun Bioinformatics
  • Identification of Drosophila MicroRNA targets.
    PLoS Biol, Vol. 1, No. 3. (December 2003)
    by A Stark, J Brennecke, RB Russell, SM Cohen
    posted to microrna prediction rna secondary structure target by eckart_bindewald on 2005-12-19 20:28:08 as **** along with 2 people and 2 groups lp2 heliopais Bioinformatics microRNA
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