Solvation effect on conformations of 1,2:dimethoxyethane: charge-dependent nonlinear response in implicit solvent models (Q41867101)

13 October 2017

Solvation effect on conformations of 1,2:dimethoxyethane: charge-dependent nonlinear response in implicit solvent models (English)

1 reference

13 October 2017

2

Karl F Freed

1 reference

13 October 2017

Abhishek K Jha

1

1 reference

PMCID

2717614

13 October 2017

language of work or name

English

0 references

publication date

1 January 2008

1 reference

Journal of Chemical Physics

13 October 2017

1 reference

13 October 2017

128

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13 October 2017

034501

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13 October 2017

3

1 reference

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

13 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717614

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717614

An Implicit Membrane Generalized Born Theory for the Study of Structure, Stability, and Interactions of Membrane Proteins

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717614

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717614

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717614

Long time dynamics of Met-enkephalin: comparison of explicit and implicit solvent models

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717614

Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717614

Helix nucleation kinetics from molecular simulations in explicit solvent

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717614

Generalized born models of macromolecular solvation effects

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717614

Effective energy function for proteins in solution

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717614

Modeling protein folding: the beauty and power of simplicity

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717614

Macroscopic models for studies of electrostatic interactions in proteins: limitations and applicability

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717614

Solvation energy in protein folding and binding

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717614

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717614

Energetic coupling between DNA bending and base pair opening

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717614

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717614

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717614

A simple method for faster nonbonded force evaluations

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717614

Constant pH molecular dynamics in generalized Born implicit solvent

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717614

Kinetics of the coil-to-helix transition on a rough energy landscape.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717614

A critical analysis of continuum electrostatics: the screened Coulomb potential--implicit solvent model and the study of the alanine dipeptide and discrimination of misfolded structures of proteins

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717614

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

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717614

The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin.

18 August 2018

1 reference

AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling.

21 January 2018

1 reference

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

21 January 2018

1 reference

Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field

21 January 2018

1 reference

Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations

21 January 2018

1 reference

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

21 January 2018

1 reference

Semianalytical treatment of solvation for molecular mechanics and dynamics

21 January 2018

1 reference

Distance and exposure dependent effective dielectric function

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717614

Beta-hairpin folding simulations in atomistic detail using an implicit solvent model

3 November 2018

1 reference

12 December 2020

All-atom fast protein folding simulations: the villin headpiece

1 reference

12 December 2020

Misfolded free energy surface of a peptide with alphabetabeta motif (1PSV) using the generalized Born solvation model

1 reference

12 December 2020

Identification and description of beta-structure in horse muscle acylphosphatase by nuclear magnetic resonance spectroscopy

1 reference

12 December 2020

Linear Interaction Energy (LIE) Models for Ligand Binding in Implicit Solvent: Theory and Application to the Binding of NNRTIs to HIV-1 Reverse Transcriptase.

1 reference

12 December 2020

Identifiers

DOI

10.1063/1.2815764

1 reference

13 October 2017

1 reference

13 October 2017

1 reference

PMCID

2717614