(Q33863202)

29 July 2017

title

X-Pol Potential: An Electronic Structure-Based Force Field for Molecular Dynamics Simulation of a Solvated Protein in Water (English)

1 reference

29 July 2017

0 references

Donald G Truhlar

3

0 references

Modesto Orozco

series ordinal

2

object named as

Modesto Orozco

1 reference

29 July 2017

Wangshen Xie

1

1 reference

29 July 2017

Jiali Gao

series ordinal

4

1 reference

29 July 2017

publication date

1 February 2009

1 reference

Journal of Chemical Theory and Computation

29 July 2017

published in

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29 July 2017

volume

5

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29 July 2017

issue

3

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29 July 2017

page(s)

459-467

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All-atom empirical potential for molecular modeling and dynamics studies of proteins

29 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873214

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873214

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873214

Incorporation of a QM/MM buffer zone in the variational double self-consistent field method

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873214

The variational explicit polarization potential and analytical first derivative of energy: Towards a next generation force field

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873214

OMx-D: semiempirical methods with orthogonalization and dispersion corrections. Implementation and biochemical application.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873214

5 July 2018

QM/MM studies of enzymes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873214

A consensus view of protein dynamics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873214

Molecular dynamics and protein function

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873214

Long-timescale simulation methods

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873214

Validation of the 53A6 GROMOS force field

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873214

How enzymes work: analysis by modern rate theory and computer simulations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873214

Force fields for protein simulations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873214

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873214

The birth of computational structural biology

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873214

Direct calculation of electron density in density-functional theory

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873214

Canonical dynamics: Equilibrium phase-space distributions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873214

Calculations of electrostatic properties in proteins. Analysis of contributions from induced protein dipoles

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873214

A priori evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873214

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873214

Dynamics of folded proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873214

Conservative Algorithm for an Adaptive Change of Resolution in Mixed Atomistic/Coarse-Grained Multiscale Simulations.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873214

The implementation of a fast and accurate QM/MM potential method in Amber

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873214

Comparison of different quantum mechanical/molecular mechanics boundary treatments in the reaction of the hepatitis C virus NS3 protease with the NS5A/5B substrate

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873214

Adaptive partitioning in combined quantum mechanical and molecular mechanical calculations of potential energy functions for multiscale simulations.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873214

Structure, thermodynamics, and liquid-vapor equilibrium of ethanol from molecular-dynamics simulations using nonadditive interactions

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873214

Ion solvation thermodynamics from simulation with a polarizable force field

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873214

Reaction-path energetics and kinetics of the hydride transfer reaction catalyzed by dihydrofolate reductase

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873214

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

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873214

IUPAC-IUB Commission on Biochemical Nomenclature. Abbreviations and symbols for the description of the conformation of polypeptide chains. Tentative rules (1969)

10 December 2018

1 reference

12 December 2020

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

1 reference

12 December 2020

Class IV charge models: A new semiempirical approach in quantum chemistry

1 reference

12 December 2020

Special Issue on Polarization

1 reference

12 December 2020

Derivation of Distributed Models of Atomic Polarizability for Molecular Simulations

1 reference

12 December 2020

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

1 reference

12 December 2020

Identifiers

DOI

10.1021/CT800239Q

1 reference

29 July 2017

1 reference

29 July 2017

1 reference