Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields

Optimizing Solute–Solute Interactions in the GLYCAM06 and CHARMM36 Carbohydrate Force Fields Using Osmotic Pressure Measurements

(2016) Wesley K. Lay et al.   Journal of Chemical Theory and Computation

Osmotic Pressure Simulations of Amino Acids and Peptides Highlight Potential Routes to Protein Force Field Parameterization

(2016) Mark S. Miller et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The structure and intermolecular forces of DNA condensates

(2016) Jejoong Yoo et al.   NUCLEIC ACIDS RESEARCH

Improved Parameterization of Amine–Carboxylate and Amine–Phosphate Interactions for Molecular Dynamics Simulations Using the CHARMM and AMBER Force Fields

(2015) Jejoong Yoo et al.   Journal of Chemical Theory and Computation

Representation of Ion–Protein Interactions Using the Drude Polarizable Force-Field

(2015) Hui Li et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Label-Free Optical Detection of Biomolecular Translocation through Nanopore Arrays

(2014) Andrey Ivankin et al.   ACS Nano

Smooth DNA Transport through a Narrowed Pore Geometry

(2014) Spencer Carson et al.   BIOPHYSICAL JOURNAL

Multisite Ion Model in Concentrated Solutions of Divalent Cations (MgCl2 and CaCl2): Osmotic Pressure Calculations

(2014) Akansha Saxena et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Multisite Ion Models That Improve Coordination and Free Energy Calculations in Molecular Dynamics Simulations

(2013) Akansha Saxena et al.   Journal of Chemical Theory and Computation

Nuclear calcium signalling in the regulation of brain function

(2013) Hilmar Bading   NATURE REVIEWS NEUROSCIENCE

Modeling and Simulation of Ion Channels

(2012) Christopher Maffeo et al.   CHEMICAL REVIEWS

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

Competitive Binding of Cations to Duplex DNA Revealed through Molecular Dynamics Simulations

(2012) Jejoong Yoo et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Divalent Cation-Induced Cluster Formation by Polyphosphoinositides in Model Membranes

(2012) Yu-Hsiu Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Atomic View of Calcium-Induced Clustering of Phosphatidylserine in Mixed Lipid Bilayers

(2011) John M. Boettcher et al.   BIOCHEMISTRY

Divalent Cation-Dependent Formation of Electrostatic PIP2 Clusters in Lipid Monolayers

(2011) Wouter G. Ellenbroek et al.   BIOPHYSICAL JOURNAL

Optimization of the CHARMM Additive Force Field for DNA: Improved Treatment of the BI/BII Conformational Equilibrium

(2011) Katarina Hart et al.   Journal of Chemical Theory and Computation

Improved Parametrization of Li+, Na+, K+, and Mg2+ Ions for All-Atom Molecular Dynamics Simulations of Nucleic Acid Systems

(2011) Jejoong Yoo et al.   Journal of Physical Chemistry Letters

Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field

(2010) Christopher M. Baker et al.   Journal of Chemical Theory and Computation

Ca2+Bridging of Apposed Phospholipid Bilayers

(2010) Zeena K. Issa et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Current Status of the AMOEBA Polarizable Force Field

(2010) Jay W. Ponder et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Optical Recognition of Converted DNA Nucleotides for Single-Molecule DNA Sequencing Using Nanopore Arrays

(2010) Ben McNally et al.   NANO LETTERS

Divalent counterion-induced condensation of triple-strand DNA

(2010) X. Qiu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microscopic Mechanics of Hairpin DNA Translocation through Synthetic Nanopores

(2009) Jeffrey Comer et al.   BIOPHYSICAL JOURNAL

Simulation of Osmotic Pressure in Concentrated Aqueous Salt Solutions

(2009) Yun Luo et al.   Journal of Physical Chemistry Letters

3D-DART: a DNA structure modelling server

(2009) M. van Dijk et al.   NUCLEIC ACIDS RESEARCH

The effect of calcium on the conformation of cobalamin transporter BtuB

(2009) Binquan Luan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The Allosteric Role of the Ca2+ Switch in Adhesion and Elasticity of C-Cadherin

(2008) Marcos Sotomayor et al.   BIOPHYSICAL JOURNAL

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations

(2008) In Suk Joung et al.   JOURNAL OF PHYSICAL CHEMISTRY B