Improving the description of interactions between Ca2+ and protein carboxylate groups, including γ-carboxyglutamic acid: revised CHARMM22* parameters

Competition among Li+, Na+, K+, and Rb+ Monovalent Ions for DNA in Molecular Dynamics Simulations Using the Additive CHARMM36 and Drude Polarizable Force Fields

(2015) Alexey Savelyev et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Equilibrium Conformational Ensemble of the Intrinsically Disordered Peptide n16N: Linking Subdomain Structures and Function in Nacre

(2014) Aaron H. Brown et al.   BIOMACROMOLECULES

Discovery, Synthesis, and Structure–Activity Relationships of Conotoxins

(2014) Kalyana B. Akondi et al.   CHEMICAL REVIEWS

Perspectives on the simulation of protein–surface interactions using empirical force field methods

(2014) Robert A. Latour   COLLOIDS AND SURFACES B-BIOINTERFACES

Balancing the Interactions of Ions, Water, and DNA in the Drude Polarizable Force Field

(2014) Alexey Savelyev et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Interaction of Charged Amino-Acid Side Chains with Ions: An Optimization Strategy for Classical Force Fields

(2014) Jens Kahlen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Ion conduction and conformational flexibility of a bacterial voltage-gated sodium channel

(2014) Céline Boiteux et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Testing of the GROMOS Force-Field Parameter Set 54A8: Structural Properties of Electrolyte Solutions, Lipid Bilayers, and Proteins

(2013) Maria M. Reif et al.   Journal of Chemical Theory and Computation

Peptides of Matrix Gla Protein Inhibit Nucleation and Growth of Hydroxyapatite and Calcium Oxalate Monohydrate Crystals

(2013) Maria Goiko et al.   PLoS One

Bio-Inspired Synthesis of Minerals for Energy, Environment, and Medicinal Applications

(2012) Sungjin Kim et al.   ADVANCED FUNCTIONAL MATERIALS

Introduction to Ion Channels and Disease

(2012) John J. Kasianowicz   CHEMICAL REVIEWS

Analytical Approaches for Studying Transporters, Channels and Porins

(2012) Joseph W. F. Robertson et al.   CHEMICAL REVIEWS

Modeling and Simulation of Ion Channels

(2012) Christopher Maffeo et al.   CHEMICAL REVIEWS

Exploring the influence of organic species on pre- and post-nucleation calcium carbonate

(2012) Paolo Raiteri et al.   FARADAY DISCUSSIONS

Ionic force field optimization based on single-ion and ion-pair solvation properties: Going beyond standard mixing rules

(2012) Maria Fyta et al.   JOURNAL OF CHEMICAL PHYSICS

The Solvation Structure of Na+ and K+ in Liquid Water Determined from High Level ab Initio Molecular Dynamics Simulations

(2012) Christopher N. Rowley et al.   Journal of Chemical Theory and Computation

Protein binding on stepped calcite surfaces: simulations of ovocleidin-17 on calcite {31.16} and {31.8}

(2012) Colin L. Freeman et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization?

(2011) Stefano Piana et al.   BIOPHYSICAL JOURNAL

Polymorph Crystal Selection by n16, an Intrinsically Disordered Nacre Framework Protein

(2011) Christopher B. Ponce et al.   CRYSTAL GROWTH & DESIGN

Definition and testing of the GROMOS force-field versions 54A7 and 54B7

(2011) Nathan Schmid et al.   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

Ab initio calculation of the potential of mean force for dissociation of aqueous Ca–Cl

(2011) Jeff Timko et al.   JOURNAL OF CHEMICAL PHYSICS

Simulation of Peptide–Surface Recognition

(2011) Rosa Di Felice et al.   Journal of Physical Chemistry Letters

Matrix Gla Protein Inhibits Ectopic Calcification by a Direct Interaction with Hydroxyapatite Crystals

(2011) Jason O’Young et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Mechanism of Ion Permeation and Selectivity in a Voltage Gated Sodium Channel

(2011) Ben Corry et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

New Nanofabrication Strategies: Inspired by Biomineralization

(2011) Joanna Aizenberg   MRS BULLETIN

Metadynamics

(2011) Alessandro Barducci et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Molecular Dynamics of Ion Hydration in the Presence of Small Carboxylated Molecules and Implications for Calcification

(2010) Laura M. Hamm et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types

(2010) Jeffery B. Klauda et al.   JOURNAL OF PHYSICAL CHEMISTRY B

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

(2009) Massimiliano Bonomi et al.   COMPUTER PHYSICS COMMUNICATIONS

Molecular Dynamics Simulations of the Dynamic and Energetic Properties of Alkali and Halide Ions Using Water-Model-Specific Ion Parameters

(2009) In Suk Joung et al.   JOURNAL OF PHYSICAL CHEMISTRY B

To Switch or Not To Switch: The Effects of Potassium and Sodium Ions on α-Poly-l-glutamate Conformations in Aqueous Solutions

(2009) Maxim V. Fedorov et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Cation specific binding with protein surface charges

(2009) B. Hess et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular Specifications of a Mineral Modulation Sequence Derived from the Aragonite-Promoting Protein n16

(2008) Sebastiano Collino et al.   BIOMACROMOLECULES

Protein- and Peptide-Directed Syntheses of Inorganic Materials

(2008) Matthew B. Dickerson et al.   CHEMICAL REVIEWS

Introduction: Biomineralization

(2008) Lara A. Estroff   CHEMICAL REVIEWS

Car–Parrinello Molecular Dynamics Simulations of CaCl2Aqueous Solutions

(2008) Teodora Todorova et al.   Journal of Chemical Theory and Computation

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

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

Cation-Specific Interactions with Carboxylate in Amino Acid and Acetate Aqueous Solutions: X-ray Absorption andab initioCalculations

(2008) Emad F. Aziz et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

Salt-Specific Stability and Denaturation of a Short Salt-Bridge-Forming α-Helix

(2008) Joachim Dzubiella   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS

Distinct Structural and Adhesive Roles of Ca2+ in Membrane Binding of Blood Coagulation Factors

(2008) Y. Zenmei Ohkubo et al.   STRUCTURE

Conantokin-P, an unusual conantokin with a long disulfide loop

(2008) Konkallu Hanumae Gowd et al.   TOXICON

Weak alkali and alkaline earth metal complexes of low molecular weight ligands in aqueous solution

(2007) Pier G. Daniele et al.   COORDINATION CHEMISTRY REVIEWS

Parameterization of Ca+2–protein interactions for molecular dynamics simulations

(2007) Elad Project et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY