Sensitivities to parameterization in the size-modified Poisson-Boltzmann equation

The Ionic Atmosphere around A-RNA: Poisson-Boltzmann and Molecular Dynamics Simulations

(2012) Serdal Kirmizialtin et al.   BIOPHYSICAL JOURNAL

RNA and Its Ionic Cloud: Solution Scattering Experiments and Atomically Detailed Simulations

(2012) Serdal Kirmizialtin et al.   BIOPHYSICAL JOURNAL

Formulation of a new and simple nonuniform size-modified poisson-boltzmann description

(2012) Alexander H. Boschitsch et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Electrostatics of Nucleic Acid Folding under Conformational Constraint

(2012) Peter C. Anthony et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

SAXS Studies of Ion–Nucleic Acid Interactions

(2011) Lois Pollack   Annual Review of Biophysics

Monovalent Cation Size and DNA Conformational Stability

(2011) Earle Stellwagen et al.   BIOCHEMISTRY

Understanding the physical basis of the salt dependence of the electrostatic binding free energy of mutated charged ligand–nucleic acid complexes

(2011) Robert C. Harris et al.   BIOPHYSICAL CHEMISTRY

A Fast and Robust Poisson–Boltzmann Solver Based on Adaptive Cartesian Grids

(2011) Alexander H. Boschitsch et al.   Journal of Chemical Theory and Computation

Differential geometry based solvation model II: Lagrangian formulation

(2011) Zhan Chen et al.   JOURNAL OF MATHEMATICAL BIOLOGY

Theoretical Assessment of the Oligolysine Model for Ionic Interactions in Protein–DNA Complexes

(2011) Marcia O. Fenley et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Mean-field description of ionic size effects with nonuniform ionic sizes: A numerical approach

(2011) Shenggao Zhou et al.   PHYSICAL REVIEW E

An RNA Aptamer with High Affinity and Broad Specificity for Zinc Finger Proteins

(2010) Tristen C. Weiss et al.   BIOCHEMISTRY

Coevolution ofDrosophila snfProtein and Its snRNA Targets

(2010) Sandra G. Williams et al.   BIOCHEMISTRY

Effects of the Nature and Concentration of Salt on the Interaction of the HIV-1 Nucleocapsid Protein with SL3 RNA

(2010) Shreyas S. Athavale et al.   BIOCHEMISTRY

Calorimetric and spectroscopic studies of aminoglycoside binding to AT-rich DNA triple helices

(2010) Hongjuan Xi et al.   BIOCHIMIE

Revisiting the Association of Cationic Groove-Binding Drugs to DNA Using a Poisson-Boltzmann Approach

(2010) Marcia O. Fenley et al.   BIOPHYSICAL JOURNAL

Comparing the Predictions of the Nonlinear Poisson−Boltzmann Equation and the Ion Size-Modified Poisson−Boltzmann Equation for a Low-Dielectric Charged Spherical Cavity in an Aqueous Salt Solution

(2010) Alexander R. J. Silalahi et al.   Journal of Chemical Theory and Computation

Differential geometry based solvation model I: Eulerian formulation

(2010) Zhan Chen et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Thermodynamics of Peptide−RNA Recognition: The Binding of a Tat Peptide to TAR RNA

(2010) Hemant Suryawanshi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Counting Ions around DNA with Anomalous Small-Angle X-ray Scattering

(2010) Suzette A. Pabit et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Thermodynamic and Kinetic Framework of Selenocysteyl-tRNASecRecognition by Elongation Factor SelB

(2009) Alena Paleskava et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Interfaces and hydrophobic interactions in receptor-ligand systems: A level-set variational implicit solvent approach

(2009) Li-Tien Cheng et al.   JOURNAL OF CHEMICAL PHYSICS

Thermodynamic Profiling of HIV RREIIB RNA–Zinc Finger Interactions

(2009) Subrata H. Mishra et al.   JOURNAL OF MOLECULAR BIOLOGY

The Influence of Monovalent Cation Size on the Stability of RNA Tertiary Structures

(2009) Dominic Lambert et al.   JOURNAL OF MOLECULAR BIOLOGY

Molecular Simulation Studies of Monovalent Counterion-Mediated Interactions in a Model RNA Kissing Loop

(2009) Alan A. Chen et al.   JOURNAL OF MOLECULAR BIOLOGY

Spectroscopic and Calorimetric Studies on the Binding of Alkaloids Berberine, Palmatine and Coralyne to Double Stranded RNA Polynucleotides

(2009) Md. Maidul Islam et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Contribution of the Closing Base Pair to Exceptional Stability in RNA Tetraloops: Roles for Molecular Mimicry and Electrostatic Factors

(2009) Joshua M. Blose et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A universal description for the experimental behavior of salt-(in)dependent oligocation-induced DNA condensation

(2009) Nikolay Korolev et al.   NUCLEIC ACIDS RESEARCH

Both helix topology and counterion distribution contribute to the more effective charge screening in dsRNA compared with dsDNA

(2009) Suzette A. Pabit et al.   NUCLEIC ACIDS RESEARCH

Mono- and Trivalent Ions around DNA: A Small-Angle Scattering Study of Competition and Interactions

(2008) Kurt Andresen et al.   BIOPHYSICAL JOURNAL

A repulsive field: advances in the electrostatics of the ion atmosphere

(2008) Vincent B Chu et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

RNA targeting through binding of small molecules: Studies on t-RNA binding by the cytotoxic protoberberine alkaloidcoralyne

(2008) Md. Maidul Islam et al.   Molecular BioSystems

3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures

(2008) Xiang-Jun Lu et al.   Nature Protocols

Electrostatic rate enhancement and transient complex of protein–protein association

(2007) Ramzi Alsallaq et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS