Predicting extreme pKa shifts in staphylococcal nuclease mutants with constant pH molecular dynamics (Q35541836)

8 August 2017

Predicting extreme pKa shifts in staphylococcal nuclease mutants with constant pH molecular dynamics (English)

1 reference

8 August 2017

Evan J Arthur

1

1 reference

8 August 2017

Joseph D Yesselman

series ordinal

2

1 reference

8 August 2017

Charles L Brooks

series ordinal

3

1 reference

8 August 2017

language of work or name

English

0 references

publication date

15 October 2011

1 reference

8 August 2017

1 reference

8 August 2017

79

1 reference

8 August 2017

12

1 reference

8 August 2017

3276-3286

1 reference

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

8 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213318

All-atom empirical potential for molecular modeling and dynamics studies of proteins

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213318

Predicting pKa values with continuous constant pH molecular dynamics

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213318

Correlation or confusion: the need for accurate terminology when comparing magnetic resonance imaging and clinical assessment of congenital vaginal anomalies

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213318

Structural origins of high apparent dielectric constants experienced by ionizable groups in the hydrophobic core of a protein

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213318

Charges in the hydrophobic interior of proteins

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213318

Mechanical coupling in myosin V: a simulation study

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213318

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213318

CHARMM: the biomolecular simulation program

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213318

λ-Dynamics free energy simulation methods

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213318

Very fast prediction and rationalization of pKa values for protein-ligand complexes

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213318

Recent advances in implicit solvent-based methods for biomolecular simulations

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213318

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213318

High Apparent Dielectric Constant Inside a Protein Reflects Structural Reorganization Coupled to the Ionization of an Internal Asp

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213318

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213318

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213318

Very fast empirical prediction and rationalization of protein pKa values

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213318

Constant pH molecular dynamics with proton tautomerism

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213318

MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213318

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213318

Structural basis of perturbed pKa values of catalytic groups in enzyme active sites

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213318

Generalized born models of macromolecular solvation effects

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213318

27 July 2018

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213318

Structural changes linked to proton translocation by subunit c of the ATP synthase

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213318

Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213318

Alternative conformations of amyloidogenic proteins govern their behavior

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213318

Production and heat stability of staphylococcal nuclease.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213318

NMR relaxation studies of the unfolding and refolding of staphylococcal nuclease at low pH.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213318

Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213318

pK values of the ionizable groups of proteins

27 July 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23195

Macroscopic electrostatic models for protonation states in proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23195

Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing-potential.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23195

Generalized born model with a simple smoothing function.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23195

Replica-exchange molecular dynamics method for protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23195

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23195

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23195

Experimental measurement of the effective dielectric in the hydrophobic core of a protein.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23195

Force Field Influence on the Observation of π-Helical Protein Structures in Molecular Dynamics Simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23195

Theory and applications of the generalized Born solvation model in macromolecular simulations

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22002886

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Constant-pH molecular dynamics using continuous titration coordinates

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22002886

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/PROT.23195

1 reference

8 August 2017

1 reference

8 August 2017

1 reference