(Q37058615)

18 August 2017

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

1 reference

18 August 2017

Lennard-Jones potential

0 references

Pengfei Li

1

0 references

author name string

Benjamin P Roberts

series ordinal

2

1 reference

PMCID

3728907

18 August 2017

Dhruva K Chakravorty

series ordinal

3

1 reference

PMCID

3728907

18 August 2017

Kenneth M Merz

series ordinal

4

1 reference

18 August 2017

1 June 2013

1 reference

Journal of Chemical Theory and Computation

18 August 2017

1 reference

18 August 2017

9

1 reference

18 August 2017

6

1 reference

18 August 2017

2733-2748

1 reference

Magnesium Ion-Water Coordination and Exchange in Biomolecular Simulations

18 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

Energetics of zinc-mediated interactions in the allosteric pathways of metal sensor proteins.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

Progress in modeling of ion effects at the vapor/water interface

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

Solution Structure of Mycobacterium tuberculosis NmtR in the Apo State: Insights into Ni(II)-Mediated Allostery

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

Insight into the cation-π interaction at the metal binding site of the copper metallochaperone CusF.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

Simulations of allosteric motions in the zinc sensor CzrA.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

Electrostatic polarization is crucial in reproducing Cu(I) interaction energies and hydration

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

GPU-accelerated molecular modeling coming of age

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

Accelerating molecular dynamic simulation on graphics processing units

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

Roles of metal ions in nucleases

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

Accelerating molecular modeling applications with graphics processors

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

The Amber biomolecular simulation programs

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

Interaction of viral proteins with metal ions: role in maintaining the structure and functions of viruses

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

Proton binding to proteins: pK(a) calculations with explicit and implicit solvent models.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

Metallochaperones: bind and deliver

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

Copper biochemistry and molecular biology

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

Zinc Finger Domains: Hypotheses and Current Knowledge

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

Zinc proteins: enzymes, storage proteins, transcription factors, and replication proteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

BioMe: biologically relevant metals.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

A Transferable Non-bonded Pairwise Force Field to Model Zinc Interactions in Metalloproteins

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

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

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

Structural and Functional Aspects of Metal Sites in Biology

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

Structural chemistry and biology of manganese metalloenzymes

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

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

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

A transferable ab initio based force field for aqueous ions.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

Metal ions in biological catalysis: from enzyme databases to general principles.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

Structural and dynamical properties of the Hg2+ aqua ion: a molecular dynamics study

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

Zn protein simulations including charge transfer and local polarization effects

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

Ion solvation thermodynamics from simulation with a polarizable force field

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

Development and validation of an integrated computational approach for the study of ionic species in solution by means of effective two-body potentials. The case of Zn2+, Ni2+, and Co2+ in aqueous solutions.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

Successful molecular dynamics simulation of two zinc complexes bridged by a hydroxide in phosphotriesterase using the cationic dummy atom method

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

Hydration of the calcium ion. An EXAFS, large-angle x-ray scattering, and molecular dynamics simulation study.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

Hydration structure and free energy of biomolecularly specific aqueous dications, including Zn2+ and first transition row metals

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

Calcium - a life and death signal

20 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3728907

The effects of charge transfer on the aqueous solvation of ions

4 December 2018

1 reference

12 December 2020

On the Solvation of the Zn2+Ion in Methanol: A Combined Quantum Mechanics, Molecular Dynamics, and EXAFS Approach

1 reference

12 December 2020

Revised Ionic Radii of Lanthanoid(III) Ions in Aqueous Solution

1 reference

12 December 2020

Effect of the Zn2+and Hg2+Ions on the Structure of Liquid Water

1 reference

12 December 2020

Hydration of Lanthanide Chloride Salts: A Quantum Chemical and Classical Molecular Dynamics Simulation Study

1 reference

12 December 2020

Bio-inorganic chemistry

1 reference

12 December 2020

Zinc binding in proteins and solution: a simple but accurate nonbonded representation

1 reference

12 December 2020

Hydrogen and Higher Shell Contributions in Zn2+, Ni2+, and Co2+Aqueous Solutions: An X-ray Absorption Fine Structure and Molecular Dynamics Study

1 reference

12 December 2020

Ions in solutions: Determining their polarizabilities from first-principles

1 reference

12 December 2020

Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure

1 reference

12 December 2020

Empirical force fields for biologically active divalent metal cations in water

1 reference

12 December 2020

Recent Advances in Zinc Enzymology

1 reference

12 December 2020

Identifiers

DOI

10.1021/CT400146W

1 reference

18 August 2017

1 reference

18 August 2017

1 reference

PMCID

3728907