(Q37277066)

19 August 2017

Molecular dynamics simulations of a DMPC bilayer using nonadditive interaction models (English)

1 reference

19 August 2017

Sandeep Patel

3

0 references

author name string

Joseph E Davis

series ordinal

1

1 reference

19 August 2017

Obaidur Rahaman

series ordinal

2

1 reference

19 August 2017

language of work or name

English

0 references

publication date

1 January 2009

1 reference

19 August 2017

1 reference

19 August 2017

96

1 reference

19 August 2017

2

1 reference

19 August 2017

385-402

1 reference

Probing Membrane Insertion Activity of Antimicrobial Polymers via Coarse-grain Molecular Dynamics

19 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

Revised charge equilibration potential for liquid alkanes.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

Modification of the CHARMM force field for DMPC lipid bilayer.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

Calculation of protein-ligand binding free energy by using a polarizable potential

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

Origin and control of superlinear polarizability scaling in chemical potential equalization methods

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

Distribution of amino acids in a lipid bilayer from computer simulations.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

Structural determinants of water permeability through the lipid membrane.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

A method to determine dielectric constants in nonhomogeneous systems: application to biological membranes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

The MARTINI force field: coarse grained model for biomolecular simulations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

Theoretical and computational models of biological ion channels

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

On the thermodynamic stability of a charged arginine side chain in a transmembrane helix

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

Using cryo-EM to measure the dipole potential of a lipid membrane.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

Aqueous solutions next to phospholipid membrane surfaces: insights from simulations.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

Simulation-based methods for interpreting x-ray data from lipid bilayers

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

Computer simulation of partitioning of ten pentapeptides Ace-WLXLL at the cyclohexane/water and phospholipid/water interfaces

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

Structure of fully hydrated fluid phase DMPC and DLPC lipid bilayers using X-ray scattering from oriented multilamellar arrays and from unilamellar vesicles.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

Complexation of phosphatidylcholine lipids with cholesterol.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

Energetics of ion conduction through the gramicidin channel

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

Mixed bilayer containing dipalmitoylphosphatidylcholine and dipalmitoylphosphatidylserine: lipid complexation, ion binding, and electrostatics

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

An Implicit Membrane Generalized Born Theory for the Study of Structure, Stability, and Interactions of Membrane Proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

Molecular dynamics simulation of a dipalmitoylphosphatidylcholine bilayer with NaCl

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

Gramicidin A channel as a test ground for molecular dynamics force fields

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

The ionization state and the conformation of Glu-71 in the KcsA K(+) channel

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

Dynamical properties of a hydrated lipid bilayer from a multinanosecond molecular dynamics simulation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

6 September 2017

Polarizable force fields

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

The dipole potential of phospholipid membranes and methods for its detection

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

Unified Approach for Molecular Dynamics and Density-Functional Theory

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

Incorporation of surface tension into molecular dynamics simulation of an interface: a fluid phase lipid bilayer membrane

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

Membrane dipole potentials, hydration forces, and the ordering of water at membrane surfaces

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

Restatement of order parameters in biomembranes: calculation of C-C bond order parameters from C-D quadrupolar splittings

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

Dipole potential of lipid membranes

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

Polarizable empirical force field for aromatic compounds based on the classical drude oscillator

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

Model conformational study of nucleic acid phosphate ester bonds. Torsional potential of dimethyl phosphate monoanion

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

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

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

Revisiting the hexane-water interface via molecular dynamics simulations using nonadditive alkane-water potentials

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

Polarization effects and charge transfer in the KcsA potassium channel.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

Comparative molecular dynamics study of lipid membranes containing cholesterol and ergosterol

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

Computer simulation of the distribution of hexane in a lipid bilayer: spatially resolved free energy, entropy, and enthalpy profiles

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

A generalized Born formalism for heterogeneous dielectric environments: application to the implicit modeling of biological membranes

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

A modified TIP3P water potential for simulation with Ewald summation

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

Effective energy function for proteins in lipid membranes

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

Molecular dynamics simulations of large integral membrane proteins with an implicit membrane model

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716476

Absolute hydration free energy scale for alkali and halide ions established from simulations with a polarizable force field

20 October 2018

1 reference

12 December 2020

Polarizable Empirical Force Field for Alkanes Based on the Classical Drude Oscillator Model

1 reference

12 December 2020

An ab Initio Study on the Torsional Surface of Alkanes and Its Effect on Molecular Simulations of Alkanes and a DPPC Bilayer

1 reference

12 December 2020

Modifying the OPLS-AA force field to improve hydration free energies for several amino acid side chains using new atomic charges and an off-plane charge model for aromatic residues

1 reference

12 December 2020

An Interpretation of Bond Lengths and a Classification of Bonds

1 reference

12 December 2020

Importance of polarization in quantum mechanics/molecular mechanics descriptions of electronic excited states: NaI(H2O)n photodissociation dynamics as a case study

1 reference

12 December 2020

Biomolecular simulations of membranes: Physical properties from different force fields

1 reference

12 December 2020

Membrane protein simulations with a united-atom lipid and all-atom protein model: lipid-protein interactions, side chain transfer free energies and model proteins

1 reference

12 December 2020

The MARTINI Coarse-Grained Force Field: Extension to Proteins.

1 reference

12 December 2020

Atomic Level Anisotropy in the Electrostatic Modeling of Lone Pairs for a Polarizable Force Field Based on the Classical Drude Oscillator

1 reference

12 December 2020

Energy Conservation in Adaptive Hybrid Atomistic/Coarse-Grain Molecular Dynamics.

1 reference

12 December 2020

Additive and Classical Drude Polarizable Force Fields for Linear and Cyclic Ethers

1 reference

12 December 2020

Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator

1 reference

12 December 2020

10.1016/J.BPJ.2008.09.048

Identifiers

DOI

1 reference

19 August 2017

1 reference

19 August 2017

PubMed publication ID

19167291

1 reference