Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH. (Q36437502)

14 August 2017

Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH. (English)

1 reference

14 August 2017

Jason A Wallace

1

1 reference

14 August 2017

Jana K Shen

series ordinal

2

1 reference

14 August 2017

language of work or name

English

0 references

publication date

1 November 2012

1 reference

Journal of Chemical Physics

14 August 2017

1 reference

14 August 2017

137

1 reference

14 August 2017

18

1 reference

14 August 2017

184105

1 reference

Continuous Constant pH Molecular Dynamics in Explicit Solvent with pH-Based Replica Exchange

14 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3511335

Constant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit Solvent

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3511335

Predicting pKa values with continuous constant pH molecular dynamics

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3511335

Constant pH replica exchange molecular dynamics in biomolecules using a discrete protonation model

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3511335

CHARMM: the biomolecular simulation program

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3511335

Progress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins: accelerated QM/MM studies of pKa, redox reactions and solvation free energies

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3511335

Control of ion selectivity in LeuT: two Na+ binding sites with two different mechanisms

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3511335

Linking folding with aggregation in Alzheimer's beta-amyloid peptides

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3511335

Effects of long-range electrostatic forces on simulated protein folding kinetics

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3511335

Folding intermediate in the villin headpiece domain arises from disruption of a N-terminal hydrogen-bonded network

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3511335

Exploring atomistic details of pH-dependent peptide folding

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3511335

Toward the accurate first-principles prediction of ionization equilibria in proteins.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3511335

Constant pH molecular dynamics with proton tautomerism

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3511335

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3511335

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3511335

Molecular dynamics simulation of highly charged proteins: comparison of the particle-particle particle-mesh and reaction field methods for the calculation of electrostatic interactions

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3511335

Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3511335

Canonical dynamics: Equilibrium phase-space distributions

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3511335

Constant pH Molecular Dynamics in Explicit Solvent with λ-Dynamics

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3511335

Toward accurate prediction of pKa values for internal protein residues: the importance of conformational relaxation and desolvation energy.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3511335

Molecular dynamics simulations of ionic and nonionic surfactant micelles with a generalized Born implicit-solvent model.

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3511335

Acidic range titration of HEWL using a constant-pH molecular dynamics method.

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3511335

Generalized ensemble and tempering simulations: a unified view.

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3511335

The influence of different treatments of electrostatic interactions on the thermodynamics of folding of peptides.

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3511335

Constant pH molecular dynamics in generalized Born implicit solvent

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3511335

Generalized born model with a simple smoothing function.

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3511335

Simulating proteins at constant pH: An approach combining molecular dynamics and Monte Carlo simulation.

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3511335

The Electrostatic Influence of Substituents on the Dissociation Constants of Organic Acids. I

21 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1063%2F1.4766352

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1063%2F1.4766352

Assessing the influence of electrostatic schemes on molecular dynamics simulations of secondary structure forming peptides

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1063%2F1.4766352

Constant-pH molecular dynamics using continuous titration coordinates

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23163362

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Simulating pH titration of a single surfactant in ionic and nonionic surfactant micelles

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23163362

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1063/1.4766352

1 reference

release_bko77admqvfhzjqolxggsdrzgu

14 August 2017

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/bko77admqvfhzjqolxggsdrzgu

mapped directly with Wikidata item

24 November 2022

based on heuristic

1 reference

14 August 2017

PubMed publication ID

23163362

1 reference