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JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2007)
Hydrophobic association of α-helices, steric dewetting, and enthalpic barriers to protein folding
Justin L. MacCallum et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
An analysis of the molecular origin of osmolyte-dependent protein stability
Jorg Rosgen et al.
PROTEIN SCIENCE (2007)
Optimized theory for simple and molecular fluids
M. Marucho et al.
JOURNAL OF CHEMICAL PHYSICS (2007)
Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum
Michael J. Schnieders et al.
JOURNAL OF CHEMICAL PHYSICS (2007)
Polarizable empirical force field for aromatic compounds based on the classical drude oscillator
Pedro E. M. Lopes et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2007)
GBr6:: A parameterization-free, accurate, analytical generalized born method
Harianto Tjong et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2007)
Tertiary structure of an RNA pseudoknot is stabilized by diffuse Mg2+ ions
Ana Maria Soto et al.
BIOCHEMISTRY (2007)
High apparent dielectric constant inside a protein reflects structural reorganization coupled to the ionization of an internal Asp
Daniel A. Karp et al.
BIOPHYSICAL JOURNAL (2007)
Calculation of pKas in RNA:: On the structural origins and functional roles of protonated nucleotides
Christopher L. Tang et al.
JOURNAL OF MOLECULAR BIOLOGY (2007)
Classification of water molecules in protein binding sites
Caterina Barillari et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2007)
QM/MM: what have we learned, where are we, and where do we go from here?
Hai Lin et al.
THEORETICAL CHEMISTRY ACCOUNTS (2007)
The finite element approximation of the nonlinear Poisson-Boltzmann equation
Long Chen et al.
SIAM JOURNAL ON NUMERICAL ANALYSIS (2007)
Effects of monovalent anions of the Hofmeister series on DPPC lipid Bilayers part II: Modeling the perpendicular and lateral equation-of-state
E. Leontidis et al.
BIOPHYSICAL JOURNAL (2007)
Optimizing the Poisson dielectric boundary with explicit solvent forces and energies: Lessons learned with atom-centered dielectric functions
Jessica M. J. Swanson et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2007)
Generalized Born model with a simple, robust molecular volume correction
John Mongan et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2007)
Ionic volumes in solution
Yizhak Marcus
BIOPHYSICAL CHEMISTRY (2006)
X-ray and neutron scattering studies of the hydration structure of alkali ions in concentrated aqueous solutions
S. Ansell et al.
BIOPHYSICAL CHEMISTRY (2006)
Ab initio quantum force field for simulations of nanostructures
A. G. Donchev
PHYSICAL REVIEW B (2006)
Polarization effects and charge transfer in the KcsA potassium channel
Denis Bucher et al.
BIOPHYSICAL CHEMISTRY (2006)
Dispersion and repulsion contributions to the solvation free energy: Comparison of quantum mechanical and classical approaches in the polarizable continuum model
Carles Curutchet et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2006)
On the fictitious-domain and interpolation formulations of the matched interface and boundary (MIB) method
Y. C. Zhou et al.
JOURNAL OF COMPUTATIONAL PHYSICS (2006)
Electrostatic, steric, and hydration interactions favor Na+ condensation around DNA compared with K+
Alexey Savelyev et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)
Second derivatives in generalized born theory
Russell A. Brown et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2006)
Particle-based implicit solvent model for biosimulations: Application to proteins and nucleic acids hydration
Nathalie Basdevant et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2006)
Dielectric studies of water clusters in cyclodextrins: Relevance to the transition between slow and fast forms of thrombin
Stephen Bone
JOURNAL OF PHYSICAL CHEMISTRY B (2006)
Inclusion of charge and polarizability fluxes provides needed physical accuracy in molecular mechanics force fields
Kim Palmo et al.
CHEMICAL PHYSICS LETTERS (2006)
Solvated docking: introducing water into the modelling of biomolecular complexes
Aalt D. J. van Dijk et al.
BIOINFORMATICS (2006)
Hydration and dewetting near fluorinated superhydrophobic plates
Xin Li et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)
Partitioning of atmospherically relevant ions between bulk water and the water/vapor interface
Laurel M. Pegram et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential
Dian Jiao et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2006)
Selective ion-binding by protein probed with the 3D-RISM theory
Norio Yoshida et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)
Mg2+-RNA interaction free energies and their relationship to the folding of RNA tertiary structures
Dan Grilley et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Trapped water molecules are essential to structural dynamics and function of a ribozyme
Maria M. Rhodes et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Toward the accurate first-principles prediction of ionization equilibria in proteins
Jana Khandogin et al.
BIOCHEMISTRY (2006)
Quality meshing of implicit solvation models of biomolecular structures
Yongjie Zhang et al.
COMPUTER AIDED GEOMETRIC DESIGN (2006)
pKD:: re-designing protein pKa values
Barbara M. Tynan-Connolly et al.
NUCLEIC ACIDS RESEARCH (2006)
Ordered surface carbons distinguish antifreeze proteins and their ice-binding regions
Andrew C. Doxey et al.
NATURE BIOTECHNOLOGY (2006)
The Hofmeister series and protein-salt interactions
Seishi Shimizu et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
An analysis of molecular packing and chemical association in liquid water using quasichemical theory
A. Paliwal et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
Assessing implicit models for nonpolar mean solvation forces: The importance of dispersion and volume terms
Jason A. Wagoner et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Counterions between charged polymers exhibit liquid-like organization and dynamics
Thomas E. Angelini et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Salt screening and specific ion adsorption determine neutral-lipid membrane interactions
Horia I. Petrache et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Local molecular field theory for effective attractions between like charged objects in systems with strong Coulomb interactions
Yng-Gwei Chen et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Protein-solvent interactions
Ninad Prabhu et al.
CHEMICAL REVIEWS (2006)
Heat capacity changes associated with nucleic acid folding
PJ Mikulecky et al.
BIOPOLYMERS (2006)
Strike a balance: Optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides
ZX Wang et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2006)
Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes
D Riccardi et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2006)
Specific ion effects at protein surfaces: A molecular dynamics study of bovine pancreatic trypsin inhibitor and horseradish peroxidase in selected salt solutions
L Vrbka et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2006)
Recent advances in molecular simulations of ion solvation at liquid interfaces
TM Chang et al.
CHEMICAL REVIEWS (2006)
Analytical electrostatics for biomolecules: Beyond the generalized Born approximation
G Sigalov et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
Balancing solvation and intramolecular interactions: Toward a consistent generalized born force field
JH Chen et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)
Conversion of trypsin into a Na+-activated enzyme
MJ Page et al.
BIOCHEMISTRY (2006)
Coupling hydrophobicity, dispersion, and electrostatics in continuum solvent models
J Dzubiella et al.
PHYSICAL REVIEW LETTERS (2006)
Improved efficiency of replica exchange simulations through use of a hybrid explicit/implicit solvation model
A Okur et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2006)
CysxHisy-Zn2+ interactions:: Possibilities and limitations of a simple pairwise force field
N Calimet et al.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2006)
Coupling nonpolar and polar solvation free energies in implicit solvent models
J Dzubiella et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
Absolute hydration free energy scale for alkali and halide ions established from simulations with a polarizable force field
G Lamoureux et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2006)
Colloquium: Scaled particle theory and the length scales of hydrophobicity
HS Ashbaugh et al.
REVIEWS OF MODERN PHYSICS (2006)
A van der Waals free energy in electrolytes revisited
B Jancovici
EUROPEAN PHYSICAL JOURNAL E (2006)
Specific ion effects in solutions of globular proteins:: Comparison between analytical models and simulation
M Boström et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2005)
Charge inversion by multivalent ions: Dependence on dielectric constant and surface-charge density
K Besteman et al.
PHYSICAL REVIEW E (2005)
Very fast empirical prediction and rationalization of protein pKa values
H Li et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2005)
The Amber biomolecular simulation programs
DA Case et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)
Water molecules in a protein cavity detected by a statistical-mechanical theory
T Imai et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2005)
Global thermodynamics of hydrophobic cavitation, dewetting, and hydration
D Ben-Amotz
JOURNAL OF CHEMICAL PHYSICS (2005)
Distributed multipole analysis: Stability for large basis sets
AJ Stone
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2005)
Protein folding, stability, and solvation structure in osmolyte solutions
J Rösgen et al.
BIOPHYSICAL JOURNAL (2005)
The coordination of uranyl in water:: A combined quantum chemical and molecular simulation study
D Hagberg et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2005)
Interactions of macromolecules with salt ions: An electrostatic theory for the Hofmeister effect
HX Zhou
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2005)
Interfaces and the driving force of hydrophobic assembly
D Chandler
NATURE (2005)
Molecular dynamics study of water penetration in staphylococcal nuclease
A Damjanovic et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2005)
Limitations of atom-centered dielectric functions in implicit solvent models
JMJ Swanson et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2005)
Charge inversion on membranes induced by multivalent-counterion fluctuations
YW Kim et al.
JOURNAL OF PHYSICS-CONDENSED MATTER (2005)
On the use of different dielectric constants for computing individual and pairwise terms in Poisson-Boltzmann studies of protein ionization equilibrium
VH Teixeira et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2005)
Charge renormalization and inversion of a highly charged lipid bilayer: Effects of dielectric discontinuities and charge correlations
S Taheri-Araghi et al.
PHYSICAL REVIEW E (2005)
Interfacial water as a Hydration fingerprint'' in the noncognate complex of BamHI
M Fuxreiter et al.
BIOPHYSICAL JOURNAL (2005)
Hydrophobic hydration from small to large lengthscales: Understanding and manipulating the crossover
S Rajamani et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
Molecular dynamics study of hydration of the protein interior
A Damjanovic et al.
COMPUTER PHYSICS COMMUNICATIONS (2005)
A quantum mechanical polarizable force field for biomolecular interactions
AG Donchev et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
Ab initio quantum chemistry:: Methodology and applications
RA Friesner
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
Energy of an ion crossing a low dielectric membrane:: the role of dispersion self-free energy
M Boström et al.
BIOPHYSICAL CHEMISTRY (2005)
Mosaic energy landscapes of liquids and the control of protein conformational dynamics by glass-forming solvents
V Lubchenko et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2005)
Density functional theory of solvation and its relation to implicit solvent models
R Ramirez et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2005)
Improving implicit solvent simulations: a Poisson-centric view
NA Baker
CURRENT OPINION IN STRUCTURAL BIOLOGY (2005)
A generalized Born formalism for heterogeneous dielectric environments: Application to the implicit modeling of biological membranes
S Tanizaki et al.
JOURNAL OF CHEMICAL PHYSICS (2005)
Hofmeister effects in surface tension of aqueous electrolyte solution
M Boström et al.
LANGMUIR (2005)
Comparative study of generalized Born models: Born radii and peptide folding
J Zhu et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2005)
Modeling water, the hydrophobic effect, and ion solvation
KA Dill et al.
ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE (2005)
Systematic size study of an insect antifreeze protein and its interaction with ice
K Liu et al.
BIOPHYSICAL JOURNAL (2005)
Interaction of viral proteins with metal ions: role in maintaining the structure and functions of viruses
UC Chaturvedi et al.
FEMS IMMUNOLOGY AND MEDICAL MICROBIOLOGY (2005)
Electrostatic correlations and fluctuations for ion binding to a finite length polyelectrolyte
ZJ Tan et al.
JOURNAL OF CHEMICAL PHYSICS (2005)
Charge distribution in the water molecule - A comparison of methods
F Martin et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)
Complicated water orientations in the minor groove of the B-DNA decamer d(CCATTAATGG)(2) observed by neutron diffraction measurements
S Arai et al.
NUCLEIC ACIDS RESEARCH (2005)
The attraction between like-charged macroions - the crucial roles of macroion geometry and charge distribution
AK Mukherjee
JOURNAL OF PHYSICS-CONDENSED MATTER (2004)
MHC-peptide binding is assisted by bound water molecules
PM Petrone et al.
JOURNAL OF MOLECULAR BIOLOGY (2004)
Functional stoichiometry and local enrichment of calmodulin interacting with Ca2+ channels
MX Mori et al.
SCIENCE (2004)
Systematic comparison of force fields for microscopic simulations of NaCl in aqueous solutions: Diffusion, free energy of hydration, and structural properties
M Patra et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
The mechanism of the type III antifreeze protein action: a computational study
C Yang et al.
BIOPHYSICAL CHEMISTRY (2004)
Recent advances in the development and application of implicit solvent models in biomolecule simulations
M Feig et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2004)
Estimation of excess solvation numbers of water and cosolvents from preferential interaction and volumetric experiments
S Shimizu
JOURNAL OF CHEMICAL PHYSICS (2004)
Role of solvent in determining conformational preferences of alanine dipeptide in water
AN Drozdov et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2004)
AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling
E Gallicchio et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
Hydration structure and free energy of biomolecularly specific aqueous dications, including Zn2+ and first transition row metals
D Asthagiri et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2004)
Estimating hydration changes upon biomolecular reactions from osmotic stress, high pressure, and preferential hydration experiments
S Shimizu
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)
Theoretical and computational models of biological ion channels
B Roux et al.
QUARTERLY REVIEWS OF BIOPHYSICS (2004)
Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures
M Feig et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations
S Patel et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
How enzymes work: Analysis by modern rate theory and computer simulations
M Garcia-Viloca et al.
SCIENCE (2004)
Effects of Hofmeister anions on DPPC Langmuir monolayers at the air-water interface
A Aroti et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2004)
Competition of hydrophobic and Coulombic interactions between nanosized solutes
J Dzubiella et al.
JOURNAL OF CHEMICAL PHYSICS (2004)
Hydrophobic collapse in multidomain protein folding
RH Zhou et al.
SCIENCE (2004)
Local properties of quantum chemical systems:: The LoProp approach
L Gagliardi et al.
JOURNAL OF CHEMICAL PHYSICS (2004)
CHARMM fluctuating charge force field for proteins: II - Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model
S Patel et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
Solvation thermodynamics of protein studied by the 3D-RISM theory
T Imai et al.
CHEMICAL PHYSICS LETTERS (2004)
On the mechanism of the Hofmeister effect
MC Gurau et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2004)
Contributions from dispersion and born self-free energies to the solvation energies of salt solutions
M Boström et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2004)
Probing hydration of monovalent cations condensed around polymeric nucleic acids
A Tikhomirova et al.
JOURNAL OF MOLECULAR BIOLOGY (2004)
Water-mediated interaction at a protein-protein interface
T Ikura et al.
CHEMICAL PHYSICS (2004)
Absence of charge inversion on rodlike polyelectrolytes with excess divalent counterions
Q Wen et al.
JOURNAL OF CHEMICAL PHYSICS (2004)
Coupled reference interaction site model/simulation approach for thermochemistry of solvation: Theory and prospects
H Freedman et al.
JOURNAL OF CHEMICAL PHYSICS (2004)
Wavelet algorithm for solving integral equations of molecular liquids. A test for the reference interaction site model
GN Chuev et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
Monovalent cations regulate DNA sequence recognition by 434 repressor
SA Mauro et al.
JOURNAL OF MOLECULAR BIOLOGY (2004)
Preferential hydration and the exclusion of cosolvents from protein surfaces
S Shimizu et al.
JOURNAL OF CHEMICAL PHYSICS (2004)
Density functional study on the structures and thermodynamic properties of small ions around polyanionic DNA
K Wang et al.
PHYSICAL REVIEW E (2004)
An efficient hybrid explicit/implicit solvent method for biomolecular simulations
MS Lee et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
Stabilization of internal charges in a protein: Water penetration or conformational change?
VP Denisov et al.
BIOPHYSICAL JOURNAL (2004)
Preferential interactions of glycine betaine and of urea with DNA: Implications for DNA hydration and for effects of these solutes on DNA stability
J Hong et al.
BIOCHEMISTRY (2004)
Crystal structure of a self-splicing group I intron with both exons
PL Adams et al.
NATURE (2004)
Standard free energy of releasing a localized water molecule from the binding pockets of proteins: Double-decoupling method
D Hamelberg et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2004)
Competitive Na+ and Rb+ binding in the minor groove of DNA
FC Marincola et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2004)
Towards an accurate representation of electrostatics in classical force fields: Efficient implementation of multipolar interactions in biomolecular simulations
C Sagui et al.
JOURNAL OF CHEMICAL PHYSICS (2004)
A semi-implicit solvent model for the simulation of peptides and proteins
N Basdevant et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
Hydration of ds-DNA and ss-DNA by neutron quasielastic scattering
M Bastos et al.
BIOPHYSICAL JOURNAL (2004)
Interactions of the KWK6 cationic peptide with short nucleic acid oligomers:: demonstration of large Coulombic end effects on binding at 0.1-0.2 M salt
JD Ballin et al.
NUCLEIC ACIDS RESEARCH (2004)
Theoretical study of interaction of winter flounder antifreeze protein with ice
A Jorov et al.
PROTEIN SCIENCE (2004)
Direct observation of charge inversion by multivalent ions as a universal electrostatic phenomenon
K Besteman et al.
PHYSICAL REVIEW LETTERS (2004)
Free energies of hydration from a generalized Born model and an ALL-atom force field
WL Jorgensen et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2004)
Molecular dynamics simulations of staphylococcal nuclease: Properties of water at the protein surface
N Smolin et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2004)
Bulk-solvent and hydration-shell fluctuations, similar to α- and β-fluctuations in glasses, control protein motions and functions
PW Fenimore et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)
Monte Carlo methods for calculating some physical properties of large molecules
M Mascagni et al.
SIAM JOURNAL ON SCIENTIFIC COMPUTING (2004)
Solvation forces on biomolecular structures: A comparison of explicit solvent and Poisson-Boltzmann models
J Wagoner et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew
HW Horn et al.
JOURNAL OF CHEMICAL PHYSICS (2004)
The determinants of carboxyl pKa values in Turkey ovomucoid third domain
H Li et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2004)
Experimentally exploring the conformational space sampled by domain reorientation in calmodulin
I Bertini et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)
Ion permeation through the α-hemolysin channel:: Theoretical studies based on Brownian dynamics and Poisson-Nernst-Plank electrodiffusion theory
SY Noskov et al.
BIOPHYSICAL JOURNAL (2004)
Hybrid boundary element and finite difference method for solving the Nonlinear poisson-boltzmann equation
AH Boschitsch et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
The non-polar solvent potential of mean force for the dimerization of alanine dipeptide: the role of solute-solvent van der Waals interactions
Y Su et al.
BIOPHYSICAL CHEMISTRY (2004)
Attraction of like-charged macroions in the strong-coupling limit
A Naji et al.
EUROPEAN PHYSICAL JOURNAL E (2004)
Ion solvation thermodynamics from simulation with a polarizable force field
A Grossfield et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2003)
Generalized born model with a simple smoothing function
WP Im et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2003)
Hofmeister effects in membrane biology:: The role of ionic dispersion potentials -: art. no. 041902
M Boström et al.
PHYSICAL REVIEW E (2003)
A simple polarizable model of water based on classical Drude oscillators
G Lamoureux et al.
JOURNAL OF CHEMICAL PHYSICS (2003)
Modular and tunable chemosensor scaffold for divalent zinc
MD Shults et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2003)
Deficiency of the Coulomb-field approximation in the generalized Born model: An improved formula for Born radii evaluation
T Grycuk
JOURNAL OF CHEMICAL PHYSICS (2003)
Exploring the origin of the ion selectivity of the KcsA potassium channel
A Burykin et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2003)
On the nonpolar hydration free energy of proteins: Surface area and continuum solvent models for the solute-solvent interaction energy
RM Levy et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2003)
Special ion effects:: Why the properties of lysozyme in salt solutions follow a Hofmeister series
M Boström et al.
BIOPHYSICAL JOURNAL (2003)
Electrostatic interactions in a peptide-RNA complex
C García-García et al.
JOURNAL OF MOLECULAR BIOLOGY (2003)
Understanding the Hofmeister effect in interactions between chaotropic anions and lipid bilayers: Molecular dynamics simulations
JN Sachs et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2003)
Like-charge attraction between polyelectrolytes induced by counterion charge density waves
TE Angelini et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)
Ion multivalence and like-charge polyelectrolyte attraction
JC Butler et al.
PHYSICAL REVIEW LETTERS (2003)
Comparison of calculation and experiment implicates significant electrostatic contributions to the binding stability of barnase and barstar
F Dong et al.
BIOPHYSICAL JOURNAL (2003)
Electrostatics and dynamics of proteins
T Simonson
REPORTS ON PROGRESS IN PHYSICS (2003)
A thermodynamic framework for the magnesium-dependent folding of RNA
VK Misra et al.
BIOPOLYMERS (2003)
An intermolecular potential model for the simulation of ice and water near the melting point:: A six-site model of H2O
H Nada et al.
JOURNAL OF CHEMICAL PHYSICS (2003)
Dynamic maintenance and visualization of molecular surfaces
CL Bajaj et al.
DISCRETE APPLIED MATHEMATICS (2003)
Nickel coordination is regulated by the DNA-bound state of NikR
PE Carrington et al.
NATURE STRUCTURAL BIOLOGY (2003)
Boundary element solution of the linear Poisson-Boltzmann equation and a multipole method for the rapid calculation of forces on macromolecules in solution
AJ Bordner et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2003)
On the evaluation and optimization of protein X-ray structures for pKa calculations
JE Nielsen et al.
PROTEIN SCIENCE (2003)
Charge-charge interactions are key determinants of the pK values of ionizable groups in ribonuclease Sa (pI=3.5) and a basic variant (pI=10.2)
DV Laurents et al.
JOURNAL OF MOLECULAR BIOLOGY (2003)
Inclusion of the ligand field contribution in a polarizable molecular mechanics: SIBFA-LF
JP Piquemal et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2003)
An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins
W Im et al.
BIOPHYSICAL JOURNAL (2003)
Role of hydration in the binding of lac repressor to DNA
MG Fried et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2002)
Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations
PY Ren et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2002)
Development of a polarizable force field for proteins via ab initio quantum chemistry:: First generation model and gas phase tests
GA Kaminski et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2002)
Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation
A Jakalian et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2002)
Coupling Poisson-Nernst-Planck and density functional theory to calculate ion flux
D Gillespie et al.
JOURNAL OF PHYSICS-CONDENSED MATTER (2002)
Effective Born radii in the generalized Born approximation: The importance of being perfect
A Onufriev et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2002)
Improved convergence of the 'atoms in molecules' multipole expansion of electrostatic interaction
L Joubert et al.
MOLECULAR PHYSICS (2002)
A reappraisal of what we have learnt during three decades of computer simulations on water
B Guillot
JOURNAL OF MOLECULAR LIQUIDS (2002)
The Poisson-Boltzmann equation for biomolecular electrostatics: a tool for structural biology
F Fogolari et al.
JOURNAL OF MOLECULAR RECOGNITION (2002)
How ions affect the structure of water
B Hribar et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2002)
Electrostatic free energy calculations using the generalized solvent boundary potential method
NK Banavali et al.
JOURNAL OF CHEMICAL PHYSICS (2002)
Accelerated Poisson-Boltzmann calculations for static and dynamic systems
R Luo et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2002)
Escaping free-energy minima
A Laio et al.
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