(Q39472349)

12 September 2017

Measuring the successes and deficiencies of constant pH molecular dynamics: a blind prediction study (English)

1 reference

12 September 2017

3

J Andrew McCammon

1 reference

12 September 2017

Sarah L Williams

1

1 reference

12 September 2017

Patrick G Blachly

series ordinal

2

1 reference

12 September 2017

language of work or name

English

0 references

publication date

30 August 2011

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12 September 2017

1 reference

12 September 2017

79

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12 September 2017

12

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12 September 2017

3381-3388

1 reference

Structural reorganization triggered by charging of Lys residues in the hydrophobic interior of a protein

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227005

Large shifts in pKa values of lysine residues buried inside a protein

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227005

Charges in the hydrophobic interior of proteins

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227005

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227005

Molecular determinants of the pKa values of Asp and Glu residues in staphylococcal nuclease

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227005

High tolerance for ionizable residues in the hydrophobic interior of proteins

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227005

Recent advances in implicit solvent-based methods for biomolecular simulations

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227005

Exploring atomistic details of pH-dependent peptide folding

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227005

Prediction and rationalization of protein pKa values using QM and QM/MM methods.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227005

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227005

Very fast empirical prediction and rationalization of protein pKa values

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227005

Constant pH molecular dynamics with proton tautomerism

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227005

Biomolecular simulations at constant pH.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227005

Proton binding to proteins: a free-energy component analysis using a dielectric continuum model.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227005

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227005

Constant-pH molecular dynamics study of protonation-structure relationship in a heptapeptide derived from ovomucoid third domain

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227005

Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227005

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227005

A Novel View of pH Titration in Biomolecules†

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227005

A self-consistent, microenvironment modulated screened coulomb potential approximation to calculate pH-dependent electrostatic effects in proteins

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227005

Electrostatic calculations of side-chain pK(a) values in myoglobin and comparison with NMR data for histidines

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227005

pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227005

Prediction of pH-dependent properties of proteins

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227005

Coupling Constant pH Molecular Dynamics with Accelerated Molecular Dynamics

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227005

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

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227005

Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227005

Molecular mechanisms of pH-driven conformational transitions of proteins: insights from continuum electrostatics calculations of acid unfolding

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227005

Constant pH molecular dynamics in generalized Born implicit solvent

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227005

Energy functions for protein design I: efficient and accurate continuum electrostatics and solvation

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227005

An empirical model for electrostatic interactions in proteins incorporating multiple geometry‐dependent dielectric constants

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227005

Semianalytical treatment of solvation for molecular mechanics and dynamics

21 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1002%2FPROT.23136

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

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1002%2FPROT.23136

Molecular dynamics with coupling to an external bath

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1002%2FPROT.23136

Simulation of protein conformational freedom as a function of pH: constant-pH molecular dynamics using implicit titration

21 January 2018

1 reference

12 December 2020

On the calculation of pKas in proteins

1 reference

12 December 2020

Constant-pH molecular dynamics using continuous titration coordinates

1 reference

12 December 2020

Is the prediction of pKa values by constant-pH molecular dynamics being hindered by inherited problems?

1 reference

12 December 2020

Identifiers

DOI

10.1002/PROT.23136

1 reference

12 September 2017

1 reference

12 September 2017

PubMed publication ID

22072520

1 reference