Overview / Neocles B. Leontis ; John SantaLucia, Jr1: |
Quantum Mechanical Calculations and Empirical Force Field Parametrization |
The Energetics of Nucleotide Ionization in Water Counterion Environments / Harshica Fernando ; Nancy S. Kim ; George A. Papadantonakis ; Pierre R. LeBreton2: |
Parameterization and Simulation of the Physical Properties of Phosphorothioate Nucleic Acids / Kenneth E. Lind ; Luke D. Sherlin ; Venkatraman Mohan ; Richard H. Griffey ; David M. Ferguson3: |
X-ray Crystallograpy |
Crystallographic Studies of RNA Internal Loops / Stephen R. Holbrook4: |
Hydrogen-Bonding Patterns Observed in the Base Pairs of Duplex Oligonucleotides / William N. Hunter ; Gordon A. Leonard ; Tom Brown5: |
Spectroscopic Studies |
Structure and Stability of DNA Containing Inverted Anomeric Centers and Polarity Reversals / James M. Aramini ; Johan H. van de Sande ; Markus W. Germann6: |
Conformational Analysis of Nucleic Acids: Problems and Solutions / Andrew N. Lane7: |
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 ; Uli Schmitz8: |
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 ; T. S. Rush III9: |
Three-Dimensional NOESY NOESY Hybrid Hybrid Matrix Refinement of a DNA Three-Way Junction / Varatharasa Thiviyanthan ; Nishantha Illangasekare ; Elliott Gozansky ; Frank Zhu ; Bruce A. Luxon ; David G. Gorenstein10: |
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. Konerding11: |
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 ; Hans J. Vogel12: |
Secondary Structure Prediction |
Thermodynamics of Duplex Formation and Mismatch Discrimination on Photolithographically Synthesized Oligonucleotide Arrays / Jonathan E. Forman ; Ian D. Walton ; David Stern ; Richard P. Rava ; Mark O. Trulson13: |
RNA Folding Dynamics: Computer Simulations by a Genetic Algorithm / A. P. Gultyaev ; F. H. D. van Batenburg ; C. W. A. Pleij14: |
An Updated Recursive Algorithm for RNA Secondary Structure Prediction with Improved Thermodynamic / David H. Mathews ; Troy C. Andre ; James Kim ; Douglas H. Turner ; Michael Zuker15: |
Molecular Dynamics Simulation |
Modeling of DNA via Molecular Dynamics Simulation: Structure, Bending, and Conformational Tansitions / D .L. Beveridge ; M. A. Young ; D. Sprous16: |
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 ; P. A. Kollman17: |
Observations on the A versus B Equilibrium in Molecular Dynamics Simulations of Duplex DNA and RNA / Alexander D. MacKerell, Jr18: |
Modeling Duplex DNA Oligonucleotides with Modified Pyrimidine Bases / John Miller ; Michael Cooney ; Karol Miaskiewicz ; Roman Osman19: |
How the TATA Box Selects Its Protein Partner / Nina Pastor ; Leonardo Pardo ; Harel Weinstein20: |
RNA Tectonics and Modular Modeling of RNA / Eric Westhof ; Benoit Masquida ; Luc Jaeger21: |
Modeling with Low-Resolution Data |
Hairpin Ribozyme Structure and Dynamics / A. R. Banerjee ; A. Berzal-Herranz ; J. Bond ; S. Butcher ; J. A. Esteban ; J. E. Heckman ; B. Sargueil, N. Wa22: |
Overview / Neocles B. Leontis ; John SantaLucia, Jr1: |
Quantum Mechanical Calculations and Empirical Force Field Parametrization |
The Energetics of Nucleotide Ionization in Water Counterion Environments / Harshica Fernando ; Nancy S. Kim ; George A. Papadantonakis ; Pierre R. LeBreton2: |
Parameterization and Simulation of the Physical Properties of Phosphorothioate Nucleic Acids / Kenneth E. Lind ; Luke D. Sherlin ; Venkatraman Mohan ; Richard H. Griffey ; David M. Ferguson3: |
X-ray Crystallograpy |
Crystallographic Studies of RNA Internal Loops / Stephen R. Holbrook4: |