Parameterization of Monovalent Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models

Thermodynamics of Transition Metal Ion Binding to Proteins

(2020) Lin Frank Song et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Systematic Parametrization of Divalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models

(2020) Zhen Li et al.   Journal of Chemical Theory and Computation

Screening Diffusion of Small Molecules in Flexible Zeolitic Imidazolate Frameworks Using a DFT-Parameterized Force Field

(2019) Ross J. Verploegh et al.   Journal of Physical Chemistry C

General Purpose Water Model Can Improve Atomistic Simulations of Intrinsically Disordered Proteins

(2019) Parviz Seifpanahi Shabane et al.   Journal of Chemical Theory and Computation

Polarizable Force Fields for Biomolecular Simulations: Recent Advances and Applications

(2019) Zhifeng Jing et al.   Annual Review of Biophysics

State of the Art and Prospects in Metal–Organic Framework (MOF)-Based and MOF-Derived Nanocatalysis

(2019) Qi Wang et al.   CHEMICAL REVIEWS

ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution

(2019) Chuan Tian et al.   Journal of Chemical Theory and Computation

RNA force field with accuracy comparable to state-of-the-art protein force fields

(2018) Dazhi Tan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot

(2018) Jorjethe Roca et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features

(2018) Tai-Sung Lee et al.   Journal of Chemical Information and Modeling

Many-body effect determines the selectivity for Ca2+and Mg2+in proteins

(2018) Zhifeng Jing et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Simulating the Chelate Effect

(2018) Arkajyoti Sengupta et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations

(2017) Zoe Cournia et al.   Journal of Chemical Information and Modeling

Accuracy limit of rigid 3-point water models

(2016) Saeed Izadi et al.   JOURNAL OF CHEMICAL PHYSICS

The ReaxFF reactive force-field: development, applications and future directions

(2016) Thomas P Senftle et al.   npj Computational Materials

Binding Enthalpy Calculations for a Neutral Host–Guest Pair Yield Widely Divergent Salt Effects across Water Models

(2015) Kaifu Gao et al.   Journal of Chemical Theory and Computation

Improved Force Field Parameters Lead to a Better Description of RNA Structure

(2015) Christina Bergonzo et al.   Journal of Chemical Theory and Computation

Systematic Parameterization of Monovalent Ions Employing the Nonbonded Model

(2015) Pengfei Li et al.   Journal of Chemical Theory and Computation

Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model

(2015) Marie L. Laury et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States

(2015) Stefano Piana et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Li-ion battery materials: present and future

(2015) Naoki Nitta et al.   Materials Today

Prediction of Solvation Free Energies with Thermodynamic Integration Using the General Amber Force Field

(2014) Silvia A. Martins et al.   Journal of Chemical Theory and Computation

Transferable Force Field for Metal–Organic Frameworks from First-Principles: BTW-FF

(2014) Jessica K. Bristow et al.   Journal of Chemical Theory and Computation

Force Field Independent Metal Parameters Using a Nonbonded Dummy Model

(2014) Fernanda Duarte et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Parameterization of Highly Charged Metal Ions Using the 12-6-4 LJ-Type Nonbonded Model in Explicit Water

(2014) Pengfei Li et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Building Water Models: A Different Approach

(2014) Saeed Izadi et al.   Journal of Physical Chemistry Letters

Building Force Fields: An Automatic, Systematic, and Reproducible Approach

(2014) Lee-Ping Wang et al.   Journal of Physical Chemistry Letters

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

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent

(2013) Pengfei Li et al.   Journal of Chemical Theory and Computation

Taking into Account the Ion-Induced Dipole Interaction in the Nonbonded Model of Ions

(2013) Pengfei Li et al.   Journal of Chemical Theory and Computation

Thermodynamically Consistent Force Fields for the Assembly of Inorganic, Organic, and Biological Nanostructures: The INTERFACE Force Field

(2013) Hendrik Heinz et al.   LANGMUIR

Metal–Organic Frameworks and Self-Assembled Supramolecular Coordination Complexes: Comparing and Contrasting the Design, Synthesis, and Functionality of Metal–Organic Materials

(2012) Timothy R. Cook et al.   CHEMICAL REVIEWS

A set of molecular models for alkali and halide ions in aqueous solution

(2012) Stephan Deublein et al.   JOURNAL OF CHEMICAL PHYSICS

Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential

(2012) Jiajing Zhang et al.   Journal of Chemical Theory and Computation

Wide-Open Flaps Are Key to Urease Activity

(2012) Benjamin P. Roberts et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

BioMe: biologically relevant metals

(2012) A. Tus et al.   NUCLEIC ACIDS RESEARCH

Computation of methodology-independent single-ion solvation properties from molecular simulations. IV. Optimized Lennard-Jones interaction parameter sets for the alkali and halide ions in water

(2011) Maria M. Reif et al.   JOURNAL OF CHEMICAL PHYSICS

Comparison of Methods to Obtain Force-Field Parameters for Metal Sites

(2011) LiHong Hu et al.   Journal of Chemical Theory and Computation

Insight into the Cation−π Interaction at the Metal Binding Site of the Copper Metallochaperone CusF

(2011) Dhruva K. Chakravorty et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structure and dynamics of hydrated Ag+: An ab initio quantum mechanical/charge field simulation

(2010) C. Markus Blauth et al.   CHEMICAL PHYSICS LETTERS

Structural Survey of Zinc-Containing Proteins and Development of the Zinc AMBER Force Field (ZAFF)

(2010) Martin B. Peters et al.   Journal of Chemical Theory and Computation

Current Status of the AMOEBA Polarizable Force Field

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

Rational design of ion force fields based on thermodynamic solvation properties

(2009) Dominik Horinek et al.   JOURNAL OF CHEMICAL PHYSICS

Force fields including charge transfer and local polarization effects: Application to proteins containing multi/heavy metal ions

(2008) Dmitri V. Sakharov et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

How do bacterial cells ensure that metalloproteins get the correct metal?

(2008) Kevin J. Waldron et al.   NATURE REVIEWS MICROBIOLOGY