Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model (Q27024746)

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English	Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model	scientific article

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17 February 2020

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Europe PubMed Central

Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model (English)

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25247054%20AND%20SRC:MED&resulttype=core&format=json

17 February 2020

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17 February 2020

author name string

Benoît Roux

3

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17 February 2020

Pedro E M Lopes

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17 February 2020

Alexander D MacKerell

4

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17 February 2020

publication date

27 August 2014

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17 February 2020

Journal of Physical Chemistry Letters

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17 February 2020

5

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17 February 2020

18

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17 February 2020

3144-3150

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PMC publication ID

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17 February 2020

Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme

1 reference

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21 March 2017

Induction of peptide bond dipoles drives cooperative helix formation in the (AAQAA)3 peptide

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28 September 2017

Induced Polarization Influences the Fundamental Forces in DNA Base Flipping.

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28 September 2017

Balancing the interactions of ions, water, and DNA in the Drude polarizable force field.

1 reference

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28 September 2017

Polarizable empirical force field for hexopyranose monosaccharides based on the classical Drude oscillator

1 reference

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28 September 2017

Force Field for Peptides and Proteins based on the Classical Drude Oscillator

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4167036

28 September 2017

The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins.

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28 September 2017

Free energetics of arginine permeation into model DMPC lipid bilayers: coupling of effective counterion concentration and lateral bilayer dimensions

1 reference

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28 September 2017

A polarizable force field of dipalmitoylphosphatidylcholine based on the classical Drude model for molecular dynamics simulations of lipids

1 reference

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28 September 2017

Systematic improvement of a classical molecular model of water

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4167036

28 September 2017

Polarizable empirical force field for acyclic polyalcohols based on the classical Drude oscillator.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4167036

28 September 2017

Temperature dependence and energetics of single ions at the aqueous liquid-vapor interface

1 reference

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28 September 2017

Derivation of fixed partial charges for amino acids accommodating a specific water model and implicit polarization

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4167036

28 September 2017

Binding structures of tri-N-acetyl-β-glucosamine in hen egg white lysozyme using molecular dynamics with a polarizable force field

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4167036

28 September 2017

The high dielectric constant of staphylococcal nuclease is encoded in its structural architecture

1 reference

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28 September 2017

Charge equilibration force fields for molecular dynamics simulations of lipids, bilayers, and integral membrane protein systems

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4167036

28 September 2017

Solvation properties of N-acetyl-β-glucosamine: molecular dynamics study incorporating electrostatic polarization

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4167036

28 September 2017

High-performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4167036

28 September 2017

Polarization Effects for Hydrogen-Bonded Complexes of Substituted Phenols with Water and Chloride Ion

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4167036

28 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4167036

28 September 2017

Polarizability rescaling and atom-based Thole scaling in the CHARMM Drude polarizable force field for ethers.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4167036

28 September 2017

QM/MM methods for biomolecular systems

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4167036

28 September 2017

The Design of a Next Generation Force Field: The X-POL Potential

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4167036

28 September 2017

Development of a polarizable intermolecular potential function (PIPF) for liquid amides and alkanes.

1 reference

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28 September 2017

Understanding the dielectric properties of liquid amides from a polarizable force field.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4167036

28 September 2017

The Additivity of the Energies of Normal Covalent Bonds

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4167036

28 September 2017

Empirical force fields for biological macromolecules: overview and issues.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4167036

28 September 2017

CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4167036

28 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4167036

28 September 2017

Development of a polarizable force field for proteins via ab initio quantum chemistry: first generation model and gas phase tests

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4167036

28 September 2017

What are the dielectric "constants" of proteins and how to validate electrostatic models?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4167036

28 September 2017

Intramolecular dielectric screening in proteins.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4167036

28 September 2017

All-atom polarizable force field for DNA based on the classical Drude oscillator model

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4167036

31 May 2018

Polarizable empirical force field for sulfur-containing compounds based on the classical Drude oscillator model

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4167036

31 May 2018

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

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4167036

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

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The medium reorganization energy for the charge transfer reactions in proteins.

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A theory for the anisotropic and inhomogeneous dielectric properties of proteins

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Development of a nonlinear classical polarization model for liquid water and aqueous solutions: COS/D.

1 reference

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Hydrogen bonding and induced dipole moments in water: predictions from the Gaussian charge polarizable model and Car-Parrinello molecular dynamics.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4167036

28 November 2018

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

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28 November 2018

Electrostatics of proteins: description in terms of two dielectric constants simultaneously.

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Polarization of water in the first hydration shell of K+ and Ca2+ ions

1 reference

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Polarization and charge transfer in the hydration of chloride ions

1 reference

https://pubmed.ncbi.nlm.nih.gov/25247054

12 December 2020

based on heuristic

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Identifiers

10.1021/JZ501315H

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Consolidated OpenCitations Corpus – April 2017

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17 February 2020

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Consolidated OpenCitations Corpus – April 2017

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2 references

Consolidated OpenCitations Corpus – April 2017

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25247054%20AND%20SRC:MED&resulttype=core&format=json

17 February 2020

PubMed publication ID

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Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

Europe PubMed Central

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17 February 2020

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