Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field (Q30494073)

16 September 2017

Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field (English)

1 reference

16 September 2017

Lennard-Jones potential

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1 reference

Christopher M Baker

1

1 reference

16 September 2017

Pedro E M Lopes

2

1 reference

16 September 2017

Xiao Zhu

3

1 reference

16 September 2017

Benoît Roux

4

1 reference

16 September 2017

Alexander D Mackerell

5

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16 September 2017

1 March 2010

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Journal of Chemical Theory and Computation

16 September 2017

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16 September 2017

6

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16 September 2017

4

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16 September 2017

1181-1198

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Efficient Simulation Method for Polarizable Protein Force Fields: Application to the Simulation of BPTI in Liquid Water.

16 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2853947

Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability. Theory and applications

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2853947

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2853947

CHARMM: the biomolecular simulation program

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2853947

Polarizable empirical force field for nitrogen-containing heteroaromatic compounds based on the classical Drude oscillator.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2853947

Revised charge equilibration potential for liquid alkanes.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2853947

Prediction of the aqueous solvation free energy of organic compounds by using autocorrelation of molecular electrostatic potential surface properties combined with response surface analysis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2853947

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2853947

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2853947

Conserved patterns in backbone torsional changes allow for single base flipping from duplex DNA with minimal distortion of the double helix

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2853947

Molecular dynamics simulations of the complete satellite tobacco mosaic virus

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2853947

A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2853947

Empirical force fields for biological macromolecules: overview and issues.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2853947

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2853947

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2853947

Simple cation-pi interaction between a phenyl ring and a protonated amine stabilizes an alpha-helix in water.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2853947

Absolute comparison of simulated and experimental protein-folding dynamics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2853947

Cation-pi interactions in ligand recognition and catalysis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2853947

Cation-pi interactions in structural biology

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2853947

Cation-pi interactions in chemistry and biology: a new view of benzene, Phe, Tyr, and Trp

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2853947

Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2853947

Interaction of the peptide bond with solvent water: a vapor phase analysis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2853947

The Structure of Liquid Benzene.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2853947

Structure, electronic circular dichroism and Raman optical activity in the gas phase and in solution: a computational and experimental investigation.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2853947

Polarizable empirical force field for the primary and secondary alcohol series based on the classical Drude model.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2853947

Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2853947

Molecular dynamics simulations of DNA with polarizable force fields: convergence of an ideal B-DNA structure to the crystallographic structure

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2853947

Force field evaluation for biomolecular simulation: free enthalpies of solvation of polar and apolar compounds in various solvents

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2853947

Solvation free energies of amino acid side chain analogs for common molecular mechanics water models.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2853947

Molecular dynamics simulations of the d(CCAACGTTGG)(2) decamer in crystal environment: comparison of atomic point-charge, extra-point, and polarizable force fields

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2853947

A generating equation for mixing rules and two new mixing rules for interatomic potential energy parameters.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2853947

Combined ab initio/empirical approach for optimization of Lennard-Jones parameters for polar-neutral compounds

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2853947

Contribution of cation-pi interactions to the stability of protein-DNA complexes

26 November 2018

1 reference

12 December 2020

Cation [M = H+, Li+, Na+, K+, Ca2+, Mg2+, NH4+, and NMe4+] interactions with the aromatic motifs of naturally occurring amino acids: a theoretical study

1 reference

12 December 2020

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

1 reference

12 December 2020

Hydration thermodynamic properties of amino acid analogues: a systematic comparison of biomolecular force fields and water models

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

Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions

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

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

1 reference

12 December 2020

SM6: A Density Functional Theory Continuum Solvation Model for Calculating Aqueous Solvation Free Energies of Neutrals, Ions, and Solute−Water Clusters

1 reference

12 December 2020

Modeling Aromatic Liquids: Toluene, Phenol, and Pyridine.

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

A Polarizable Force Field and Continuum Solvation Methodology for Modeling of Protein-Ligand Interactions

1 reference

12 December 2020

Affinities of amino acid side chains for solvent water

1 reference

12 December 2020

Identifiers

DOI

10.1021/CT9005773

1 reference

release_hjmv6yak5fbpbjwebvdhqpjlee

16 September 2017

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/hjmv6yak5fbpbjwebvdhqpjlee

24 November 2022

mapped directly with Wikidata item

1 reference

16 September 2017

PubMed publication ID

20401166

1 reference