(Q36736171)

English

Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation

scientific article published on 27 January 2007

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scholarly article

1 reference

Europe PubMed Central

PMC publication ID

16 August 2017

Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation (English)

1 reference

Europe PubMed Central

PMC publication ID

16 August 2017

1 reference

based on heuristic

inferred from title

author name string

Daniel R Roe

1

1 reference

Europe PubMed Central

PMC publication ID

16 August 2017

Asim Okur

2

1 reference

Europe PubMed Central

PMC publication ID

16 August 2017

Lauren Wickstrom

3

1 reference

Europe PubMed Central

PMC publication ID

16 August 2017

Viktor Hornak

4

1 reference

Europe PubMed Central

PMC publication ID

16 August 2017

Carlos Simmerling

5

1 reference

Europe PubMed Central

PMC publication ID

16 August 2017

language of work or name

0 references

publication date

27 January 2007

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Europe PubMed Central

PMC publication ID

16 August 2017

number of pages

12

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inferred from page(s)

Journal of Physical Chemistry B

1 reference

Europe PubMed Central

PMC publication ID

16 August 2017

111

1 reference

Europe PubMed Central

PMC publication ID

16 August 2017

7

1 reference

Europe PubMed Central

PMC publication ID

16 August 2017

1846-1857

1 reference

Europe PubMed Central

PMC publication ID

16 August 2017

Implicit solvent models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4810457

29 September 2017

Comparison of multiple Amber force fields and development of improved protein backbone parameters

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4810457

29 September 2017

Polyproline II conformation is one of many local conformational states and is not an overall conformation of unfolded peptides and proteins.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4810457

29 September 2017

The Amber biomolecular simulation programs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4810457

29 September 2017

Improving implicit solvent simulations: a Poisson-centric view

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4810457

29 September 2017

Implementation and testing of stable, fast implicit solvation in molecular dynamics using the smooth-permittivity finite difference Poisson-Boltzmann method

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4810457

29 September 2017

Unfolded state of polyalanine is a segmented polyproline II helix.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4810457

29 September 2017

Recent advances in the development and application of implicit solvent models in biomolecule simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4810457

29 September 2017

Exploring protein native states and large-scale conformational changes with a modified generalized born model

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4810457

29 September 2017

Hydration dynamics near a model protein surface.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4810457

29 September 2017

Simulation of the folding equilibrium of α-helical peptides: A comparison of the generalized Born approximation with explicit solvent

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4810457

29 September 2017

Free energy landscape of protein folding in water: Explicit vs. implicit solvent

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4810457

29 September 2017

Solvent viscosity dependence of the folding rate of a small protein: distributed computing study

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4810457

29 September 2017

Can a continuum solvent model reproduce the free energy landscape of a beta -hairpin folding in water?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4810457

29 September 2017

Effective Born radii in the generalized Born approximation: the importance of being perfect

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4810457

29 September 2017

Polyproline II structure in a sequence of seven alanine residues.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4810457

29 September 2017

Tryptophan zippers: Stable, monomeric -hairpins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4810457

29 September 2017

Generalized born models of macromolecular solvation effects

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4810457

29 September 2017

VMD: visual molecular dynamics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4810457

29 September 2017

Classical electrostatics in biology and chemistry

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4810457

29 September 2017

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4810457

29 September 2017

A precise analytical method for calculating the electrostatic energy of macromolecules in aqueous solution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4810457

28 June 2018

Optimized Radii for Poisson-Boltzmann Calculations with the AMBER Force Field

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4810457

5 September 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4810457

5 September 2018

Investigation of Salt Bridge Stability in a Generalized Born Solvent Model.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4810457

5 September 2018

Incorporating variable dielectric environments into the generalized Born model

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4810457

5 September 2018

Free energy surfaces of beta-hairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4810457

5 September 2018

Polyproline II helix is the preferred conformation for unfolded polyalanine in water

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4810457

5 September 2018

Accelerated Poisson-Boltzmann calculations for static and dynamic systems

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4810457

5 September 2018

Computer simulations with explicit solvent: recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4810457

5 September 2018

Improved Efficiency of Replica Exchange Simulations through Use of a Hybrid Explicit/Implicit Solvation Model

1 reference

https://pubmed.ncbi.nlm.nih.gov/17256983

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Comparative study of generalized born models: Born radii and peptide folding

1 reference

https://pubmed.ncbi.nlm.nih.gov/17256983

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1021/JP066831U

1 reference

Europe PubMed Central

PMC publication ID

16 August 2017

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

16 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

16 August 2017

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