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Journal Abstract Search

173 related items for PubMed ID: 17401565

  • 1. RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone.
    Wang X, Kapral G, Murray L, Richardson D, Richardson J, Snoeyink J.
    J Math Biol; 2008 Jan; 56(1-2):253-78. PubMed ID: 17401565
    [Abstract] [Full Text] [Related]

  • 2. RNA backbone is rotameric.
    Murray LJ, Arendall WB, Richardson DC, Richardson JS.
    Proc Natl Acad Sci U S A; 2003 Nov 25; 100(24):13904-9. PubMed ID: 14612579
    [Abstract] [Full Text] [Related]

  • 3. RNA backbone rotamers--finding your way in seven dimensions.
    Murray LJ, Richardson JS, Arendall WB, Richardson DC.
    Biochem Soc Trans; 2005 Jun 25; 33(Pt 3):485-7. PubMed ID: 15916548
    [Abstract] [Full Text] [Related]

  • 4. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids.
    Davis IW, Leaver-Fay A, Chen VB, Block JN, Kapral GJ, Wang X, Murray LW, Arendall WB, Snoeyink J, Richardson JS, Richardson DC.
    Nucleic Acids Res; 2007 Jul 25; 35(Web Server issue):W375-83. PubMed ID: 17452350
    [Abstract] [Full Text] [Related]

  • 5. Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms.
    Word JM, Lovell SC, LaBean TH, Taylor HC, Zalis ME, Presley BK, Richardson JS, Richardson DC.
    J Mol Biol; 1999 Jan 29; 285(4):1711-33. PubMed ID: 9917407
    [Abstract] [Full Text] [Related]

  • 6. Computational Methods for RNA Structure Validation and Improvement.
    Jain S, Richardson DC, Richardson JS.
    Methods Enzymol; 2015 Jan 29; 558():181-212. PubMed ID: 26068742
    [Abstract] [Full Text] [Related]

  • 7. RCrane: semi-automated RNA model building.
    Keating KS, Pyle AM.
    Acta Crystallogr D Biol Crystallogr; 2012 Aug 29; 68(Pt 8):985-95. PubMed ID: 22868764
    [Abstract] [Full Text] [Related]

  • 8. MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes.
    Davis IW, Murray LW, Richardson JS, Richardson DC.
    Nucleic Acids Res; 2004 Jul 01; 32(Web Server issue):W615-9. PubMed ID: 15215462
    [Abstract] [Full Text] [Related]

  • 9. Correcting pervasive errors in RNA crystallography through enumerative structure prediction.
    Chou FC, Sripakdeevong P, Dibrov SM, Hermann T, Das R.
    Nat Methods; 2013 Jan 01; 10(1):74-6. PubMed ID: 23202432
    [Abstract] [Full Text] [Related]

  • 10. RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures.
    Antczak M, Zok T, Osowiecki M, Popenda M, Adamiak RW, Szachniuk M.
    BMC Bioinformatics; 2018 Aug 22; 19(1):304. PubMed ID: 30134831
    [Abstract] [Full Text] [Related]

  • 11. FR3D: finding local and composite recurrent structural motifs in RNA 3D structures.
    Sarver M, Zirbel CL, Stombaugh J, Mokdad A, Leontis NB.
    J Math Biol; 2008 Jan 22; 56(1-2):215-52. PubMed ID: 17694311
    [Abstract] [Full Text] [Related]

  • 12. Modeling the three-dimensional structure of RNA using discrete nucleotide conformational sets.
    Gautheret D, Major F, Cedergren R.
    J Mol Biol; 1993 Feb 20; 229(4):1049-64. PubMed ID: 7680379
    [Abstract] [Full Text] [Related]

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  • 14. New tools in MolProbity validation: CaBLAM for CryoEM backbone, UnDowser to rethink "waters," and NGL Viewer to recapture online 3D graphics.
    Prisant MG, Williams CJ, Chen VB, Richardson JS, Richardson DC.
    Protein Sci; 2020 Jan 20; 29(1):315-329. PubMed ID: 31724275
    [Abstract] [Full Text] [Related]

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  • 16. Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place.
    Headd JJ, Immormino RM, Keedy DA, Emsley P, Richardson DC, Richardson JS.
    J Struct Funct Genomics; 2009 Mar 20; 10(1):83-93. PubMed ID: 19002604
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  • 19. Nucleic acid structure analysis: a users guide to a collection of new analysis programs.
    Babcock MS, Pednault EP, Olson WK.
    J Biomol Struct Dyn; 1993 Dec 20; 11(3):597-628. PubMed ID: 7510497
    [Abstract] [Full Text] [Related]

  • 20. Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation.
    Word JM, Lovell SC, Richardson JS, Richardson DC.
    J Mol Biol; 1999 Jan 29; 285(4):1735-47. PubMed ID: 9917408
    [Abstract] [Full Text] [Related]

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