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  1. No Access

    Article

    Metropolis Monte Carlo calculations of DNA structure using internal coordinates and NMR distance restraints: An alternative method for generating a high-resolution solution structure

    A new method, a restrained Monte Carlo (rMC) calculation, is demonstrated for generating high-resolution structures of DNA oligonucleotides in solution from interproton distance restraints and bounds derived f...

    Nikolai B. Ulyanov, Uli Schmitz, Thomas L. James in Journal of Biomolecular NMR (1993)

  2. No Access

    Article

    Interproton distance bounds from 2D NOE intensities: Effect of experimental noise and peak integration errors

    The effect of experimental and integration errors on the calculations in interproton distances from NOE intensities is examined. It is shown that NOE intensity errors can have a large impact on the distances d...

    He Liu, H. Peter Spielmann, Nikolai B. Ulyanov… in Journal of Biomolecular NMR (1995)

  3. No Access

    Article

    The dynamic NMR structure of the TΨC-loop: Implications for the specificity of tRNA methylation

    tRNA (m5U54)-methyltransferase (RUMT) catalyzes the S-adenosylmethionine-dependentmethylation of uridine-54 in the TΨC-loop of all transfer RNAs in E. coli to form the 54-ribosylthymine residue. However, in al...

    Letitia J. Yao, Thomas L. James, James T. Kealey… in Journal of Biomolecular NMR (1997)

  4. No Access

    Article

    Restrained molecular dynamics of solvated duplex DNA using the particle mesh Ewald method

    Restrained and unrestrained aqueous solution molecular dynamics simulations applying the particle mesh Ewald (PME) method to DNA duplex structures previously determined via in vacuo restrained molecular dynami...

    David E. Konerding, Thomas E. Cheatham III, Peter A. Kollman… in Journal of Biomolecular NMR (1999)

  5. No Access

    Article

    Determination of the populations and structures of multiple conformers in an ensemble from NMR data: Multiple-copy refinement of nucleic acid structures using floating weights

    A new algorithm is presented for determination of structural conformers and their populations based on NMR data. Restrained Metropolis Monte Carlo simulations or restrained energy minimizations are performed f...

    Adrian Görler, Nikolai B. Ulyanov, Thomas L. James in Journal of Biomolecular NMR (2000)

  6. No Access

    Article

    High-resolution NMR structure of an AT-rich DNA sequence

    We have determined, by proton NMR and complete relaxation matrix methods, the high-resolution structure of a DNA oligonucleotide in solution with nine contiguous AT base pairs. The stretch of AT pairs, TAATTAT...

    Nikolai B. Ulyanov, William R. Bauer, Thomas L. James in Journal of Biomolecular NMR (2002)

  7. No Access

    Article

    Resonance assignment of the first and second KH (hnRNP-K homology) domains of human poly(C)-binding protein-2 (PCBP2)

    Zhihau Du, Sebastian Fenn, Thomas L. James in Journal of Biomolecular NMR (2007)