Molecular Modeling of Nucleic Acids

Content: The energetics of nucleotide ionization in water-counterion environments / Harshica Fernando, Nancy S. Kim, George A. Papadantonakis, and Pierre R. LeBreton -- Parameterization and simulation of the physical properties of phosphorothioate nucleic acids / Kenneth E. Lind, Luke D. Sherlin, Venkatraman Mohan, Richard H. Griffey, and David M. Ferguson -- Crystallographic studies of RNA internal loops / Stephen R. Holbrook -- Hydrogen-bonding patterns observed in the base pairs of duplex oligonucleotides / William N. Hunter, Gordon A. Leonard, and Tom Brown -- Structure and stability of DNA containing inverted anomeric centers and polarity reversals / James M. Aramini, Johan H. van de Sande, and Markus W. Germann -- Conformational analysis of nucleic acids : problems and solutions / Andrew N. Lane -- NMR structure determination of a 28-nucleotide signal recognition particle RNA with complete relaxation matrix methods using corrected nuclear Overhauser effect intensities / Peter Lukavsky, Todd M. Billeci, Thomas L. James, and Uli Schmitz -- Molecular modeling of DNA using Raman and NMR data, and the nuclease activity of 1,10-phenanthroline-copper ion / W.L. Peticolas, M. Ghomi, A. Spassky, E.M. Evertsz, and T.S. Rush, III -- Three-dimensional NOESY-NOESY hybrid-hybrid matrix refinement of a DNA three-way junction / Varatharasa Thiviyanthan, Nishantha Illangasekare, Elliott Gozansky, Frank Zhu, Neocles B. Leontis, Bruce A. Luxon, and David G. Gorenstein -- Determination of structural ensembles from NMR data : conformational sampling and probability assessment / Nikolai B. Ulyanov, Anwer Mujeeb, Alessandro Donati, Patrick Furrer, He Liu, Shauna Farr-Jones, David E. Konerding, Uli Schmitz, and Thomas L. James -- NMR studies of the binding of an SPXX-containing peptide from high-molecular-weight basic nuclear proteins to an A-T rich DNA hairpin / Ning Zhou and Hans J. Vogel -- Thermodynamics of duplex formation and mismatch discrimination on photolithographically synthesized oligonucleotide arrays / Jonathan E. Forman, Ian D. Walton, David Stern, Richard P. Rava, and Mark O. Trulson -- RNA folding dynamics : computer simulations by a genetic algorithm / A.P. Gultyaev, F.H.D. van Batenburg, and C.W.A. Pleij -- An updated recursive algorithm for RNA secondary structure prediction with improved thermodynamic parameters / David H. Mathews, Troy C. Andre, James Kim, Douglas H. Turner, and Michael Zuker -- Modeling of DNA via molecular dynamics simulation : structure, bending, and conformational t[r]ansitions / D.L. Beveridge, M.A. Young, and D. Sprous -- Molecular dynamics simulations on nucleic acid systems using the Cornell et al. force field and particle mesh Ewald electrostatics / T.E. Cheatham, III, J.L. Miller, T.I. Spector, P. Cieplak, and P.A. Kollman -- Observations on the A versus B equilibrium in molecular dynamics simulations of duplex DNA and RNA / Alexander D. MacKerell, Jr. -- Modeling duplex DNA oligonucleotides with modified pyrimidine bases / John Miller, Michael Cooney, Karol Miaskiewicz, and Roman Osman -- How the TATA box selects its protein partner / Nina Pastor, Leonardo Pardo, and Harel Weinstein -- RNA tectonics and modular modeling of RNA / Eric Westhof, Benoît Masquida, and Luc Jaeger -- Hairpin ribozyme structure and dynamics / A.R. Banerjee, A. Berzal-Herranz, J. Bond, S. Butcher, J.A. Esteban, J.E. Heckman, B. Sargueil, N. Walter, and J.M. Burke -- Molecular modeling studies on the ribosome / Stephen C. Harvey, Margaret S. VanLoock, Thomas R. Rasterwood, and Robert K.-Z. Tan -- Modeling unusual nucleic acid structures / Thomas J. Macke and David A. Case -- Computer RNA three-dimensional modeling from low-resolution data and multiple-sequence information / François Major, Sébastien Lemieux, and Abdelmjid Ftouhi -- Comparative modeling of the three-dimensional structure of signal recognition particle RNA / Christian Zwieb, Krishne Gowda, Niels Larsen, and Florian Müller.