Polarizable Force Fields: History, Test Cases, and Prospects (Q38658999)

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English	Polarizable Force Fields: History, Test Cases, and Prospects	scientific article

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scholarly article

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Europe PubMed Central

5 September 2017

Polarizable Force Fields: History, Test Cases, and Prospects (English)

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stated in

Europe PubMed Central

5 September 2017

Andrei V Pisliakov

3

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Arieh Warshel

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1

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Arieh Warshel

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stated in

Europe PubMed Central

5 September 2017

Mitsunori Kato

2

1 reference

stated in

Europe PubMed Central

5 September 2017

1 November 2007

1 reference

stated in

Europe PubMed Central

5 September 2017

Journal of Chemical Theory and Computation

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stated in

Europe PubMed Central

5 September 2017

3

1 reference

stated in

Europe PubMed Central

5 September 2017

6

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stated in

Europe PubMed Central

5 September 2017

2034-2045

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Europe PubMed Central

5 September 2017

Control of the redox potential of cytochrome c and microscopic dielectric effects in proteins.

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Water and ion permeation in bAQP1 and GlpF channels: a kinetic Monte Carlo study

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Energetics of ion permeation through membrane channels. Solvation of Na+ by gramicidin A.

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A simple polarizable model of water based on classical Drude oscillators

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On the energetics of conformational changes and pH dependent redox behaviour of electron transfer proteins

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Cooperative effects in simulated water

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Free energy of charges in solvated proteins: microscopic calculations using a reversible charging process

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Modeling electrostatic effects in proteins

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Structural determinants of proton blockage in aquaporins

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Calculations of electrostatic interactions in biological systems and in solutions

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Dipoles localized at helix termini of proteins stabilize charges

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Quantum Mechanical Dynamical Effects in an Enzyme-Catalyzed Proton Transfer Reaction

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A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions

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

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A computational study of ion binding and protonation states in the KcsA potassium channel.

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Ion channels, permeation, and electrostatics: insight into the function of KcsA.

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Magnesium-cationic dummy atom molecules enhance representation of DNA polymerase beta in molecular dynamics simulations: improved accuracy in studies of structural features and mutational effects

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Predictions of the properties of water from first principles

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Computer simulation of the triosephosphate isomerase catalyzed reaction

1 reference

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Electrostatic interactions in macromolecules: theory and applications

1 reference

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Water properties from first principles: simulations by a general-purpose quantum mechanical polarizable force field

1 reference

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Computer modelling of enzyme catalysed reaction mechanisms.

1 reference

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Electrostatic effects in macromolecules: fundamental concepts and practical modeling.

1 reference

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Theoretical modeling of enzyme catalytic power: analysis of "cratic" and electrostatic factors in catechol O-methyltransferase

1 reference

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Remarkable rate enhancement of orotidine 5'-monophosphate decarboxylase is due to transition-state stabilization rather than to ground-state destabilization.

1 reference

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The dynamics and energetics of water permeation and proton exclusion in aquaporins

1 reference

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The low barrier hydrogen bond (LBHB) proposal revisited: the case of the Asp... His pair in serine proteases

1 reference

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Using a charging coordinate in studies of ionization induced partial unfolding

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Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches

1 reference

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Exploring the origin of the ion selectivity of the KcsA potassium channel

1 reference

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Control of reduction potential by protein matrix: lesson from a spherical protein model

1 reference

11 October 2022

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Are unit charges always negligible?

1 reference

11 October 2022

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Simulations of ion permeation through a potassium channel: molecular dynamics of KcsA in a phospholipid bilayer

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CT700127W

Aquaporin water channels: molecular mechanisms for human diseases

1 reference

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Protein Control of Redox Potentials of Ironminus signSulfur Proteins

1 reference

11 October 2022

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Computer simulation and analysis of the reaction pathway of triosephosphate isomerase

1 reference

11 October 2022

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Structural determinants of water permeation through aquaporin-1

1 reference

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Voltage-gated proton channels and other proton transfer pathways

1 reference

11 October 2022

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Computer simulations of enzyme catalysis: methods, progress, and insights

1 reference

11 October 2022

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Ion solvation thermodynamics from simulation with a polarizable force field

1 reference

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Cooperative Hydrogen Bonding and Enzyme Catalysis

1 reference

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A quantum mechanical polarizable force field for biomolecular interactions

1 reference

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Energetics of electron-transfer and protonation reactions of the quinones in the photosynthetic reaction center of Rhodopseudomonas viridis.

1 reference

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Structural basis of water-specific transport through the AQP1 water channel

1 reference

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Energetic optimization of ion conduction rate by the K+ selectivity filter

1 reference

11 October 2022

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Electrostatic Tuning of Permeation and Selectivity in Aquaporin Water Channels

1 reference

11 October 2022

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Electrostatic origin of the catalytic power of enzymes and the role of preorganized active sites

1 reference

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Energetics of enzyme catalysis

1 reference

11 October 2022

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Solvation, reorganization energy, and biological catalysis

1 reference

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The pore helix dipole has a minor role in inward rectifier channel function

1 reference

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Intrinsic pKas of ionizable residues in proteins: an explicit solvent calculation for lysozyme

1 reference

11 October 2022

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Simulations of ion current in realistic models of ion channels: the KcsA potassium channel

1 reference

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Insights into properties and energetics of iron-sulfur proteins from simple clusters to nitrogenase

1 reference

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Ion permeation mechanism of the potassium channel

1 reference

11 October 2022

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Conversion of light energy to electrostatic energy in the proton pump of Halobacterium halobium

1 reference

11 October 2022

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Polarizable force fields

1 reference

11 October 2022

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

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CT700127W

On the origin of the electrostatic barrier for proton transport in aquaporin

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CT700127W

Roles of electrostatic interaction in proteins.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CT700127W

Control of the selectivity of the aquaporin water channel family by global orientational tuning

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CT700127W

The Grotthuss mechanism

1 reference

11 October 2022

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The contribution of electrostatic and van der Waals interactions to the stereospecificity of the reaction catalyzed by lactate dehydrogenase

1 reference

11 October 2022

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The mechanism of proton exclusion in aquaporin channels

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CT700127W

What really prevents proton transport through aquaporin? Charge self-energy versus proton wire proposals

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CT700127W

Direct evidence for the exploitation of an alpha-helix in the catalytic mechanism of triosephosphate isomerase

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CT700127W

Molecular dynamics study of the KcsA potassium channel

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CT700127W

Dynamics of biochemical and biophysical reactions: insight from computer simulations

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CT700127W

The cavity and pore helices in the KcsA K+ channel: electrostatic stabilization of monovalent cations.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CT700127W

Structure and function of channels and channelogs as studied by computational chemistry

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CT700127W

Electrostatic effects in proteins

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CT700127W

Development of a simple, self-consistent polarizable model for liquid water

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CT700127W

Structural origins of redox potentials in Fe-S proteins: electrostatic potentials of crystal structures

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CT700127W

The Mechanism of Proton Exclusion in the Aquaporin-1 Water Channel

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CT700127W

Energetics of charge-charge interactions in proteins.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CT700127W

Energetics of ion conduction through the gramicidin channel

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CT700127W

Climatic impact of tropical lowland deforestation on nearby montane cloud forests

1 reference

11 October 2022

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

1 reference

11 October 2022

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Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CT700127W

Studies of the reduction and protonation behavior of tetraheme cytochromes using atomic detail

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CT700127W

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

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CT700127W

On the role of the active site helix in papain, an AB initio molecular orbital study

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CT700127W

Relation between the local field at large distances from a charge or dipole and the dielectric constant.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CT700127W

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

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CT700127W

The alpha-helix dipole and the properties of proteins

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CT700127W

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DOI

10.1021/CT700127W

1 reference

stated in

Europe PubMed Central

5 September 2017

1 reference

Europe PubMed Central

PubMed ID

26636199

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5 September 2017

Polarizable Force Fields: History, Test Cases, and Prospects (Q38658999)

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Polarizable Force Fields: History, Test Cases, and Prospects (Q38658999)

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