(Q35086870)

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Polarizable Simulations with Second order Interaction Model (POSSIM) force field: Developing parameters for alanine peptides and protein backbone

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scholarly article

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Europe PubMed Central

PubMed publication ID

6 August 2017

Polarizable Simulations with Second order Interaction Model (POSSIM) force field: Developing parameters for alanine peptides and protein backbone (English)

1 reference

Europe PubMed Central

PubMed publication ID

6 August 2017

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author name string

Sergei Y Ponomarev

1

1 reference

Europe PubMed Central

PubMed publication ID

6 August 2017

George A Kaminski

2

1 reference

Europe PubMed Central

PubMed publication ID

6 August 2017

publication date

1 May 2011

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Europe PubMed Central

PubMed publication ID

6 August 2017

Journal of Chemical Theory and Computation

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Europe PubMed Central

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6 August 2017

7

1 reference

Europe PubMed Central

PubMed publication ID

6 August 2017

5

1 reference

Europe PubMed Central

PubMed publication ID

6 August 2017

1415-1427

1 reference

Europe PubMed Central

PubMed publication ID

6 August 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=3129858

8 July 2018

Polarizable Simulations with Second order Interaction Model - force field and software for fast polarizable calculations: Parameters for small model systems and free energy calculations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129858

8 July 2018

Reproducing basic pKa values for turkey ovomucoid third domain using 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=3129858

8 July 2018

Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129858

8 July 2018

Developing polarized protein-specific charges for protein dynamics: MD free energy calculation of pKa shifts for Asp26/Asp20 in thioredoxin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129858

8 July 2018

Electrostatic polarization is crucial for reproducing pKa shifts of carboxylic residues in Turkey ovomucoid third domain.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129858

8 July 2018

An improved algorithm for analytical gradient evaluation in resolution-of-the-identity second-order Møller-Plesset perturbation theory: Application to alanine tetrapeptide conformational analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129858

8 July 2018

Conformational dynamics of sialyl Lewisx in aqueous solution and its interaction with selectinE. A study by molecular dynamics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129858

8 July 2018

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=3129858

8 July 2018

Unusually stable helix formation in short alanine-based peptides

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129858

8 July 2018

The mechanism of alpha-helix formation by peptides

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129858

8 July 2018

Pseudospectral Local Second-Order Møller-Plesset Methods for Computation of Hydrogen Bonding Energies of Molecular Pairs.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129858

27 September 2018

Polarization and polarizability assessed by protein amide acidity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129858

27 September 2018

On the helix-coil transition in alanine based polypeptides in gas phase.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129858

27 September 2018

Accurate prediction of absolute acidity constants in water with a polarizable force field: substituted phenols, methanol, and imidazole.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129858

27 September 2018

Temperature and pressure effects on conformational equilibria of alanine dipeptide in aqueous solution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129858

27 September 2018

A computationally inexpensive modification of the point dipole electrostatic polarization model for molecular simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129858

27 September 2018

A simple, efficient polarizable coarse-grained water model for molecular dynamics simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129858

16 November 2018

Electronic polarization is important in stabilizing the native structures of proteins

1 reference

https://pubmed.ncbi.nlm.nih.gov/21743799

12 December 2020

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Identifiers

10.1021/CT1007197

1 reference

Europe PubMed Central

PubMed publication ID

6 August 2017

PMC publication ID

1 reference

Europe PubMed Central

PubMed publication ID

6 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

6 August 2017

ResearchGate publication ID

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