(Q35561768)

8 August 2017

title

Developing hybrid approaches to predict pKa values of ionizable groups (English)

1 reference

8 August 2017

Shawn Witham

1

1 reference

8 August 2017

Kemper Talley

2

1 reference

8 August 2017

Lin Wang

3

1 reference

8 August 2017

Zhe Zhang

4

1 reference

8 August 2017

Subhra Sarkar

5

1 reference

8 August 2017

Daquan Gao

6

1 reference

8 August 2017

Wei Yang

7

1 reference

8 August 2017

Emil Alexov

8

1 reference

8 August 2017

language of work or name

English

0 references

publication date

8 July 2011

1 reference

8 August 2017

1 reference

8 August 2017

volume

79

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8 August 2017

issue

12

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8 August 2017

page(s)

3389-3399

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Predicting pKa values with continuous constant pH molecular dynamics

8 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3220190

Electrostatics in proteins and protein-ligand complexes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3220190

On the pH-optimum of activity and stability of proteins

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3220190

Adaptations of proteins to cellular and subcellular pH

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3220190

Evidence for the adaptation of protein pH-dependence to subcellular pH.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3220190

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3220190

MCCE2: improving protein pKa calculations with extensive side chain rotamer sampling

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3220190

Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3220190

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3220190

Cofilin is a pH sensor for actin free barbed end formation: role of phosphoinositide binding

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3220190

Backbone relaxation coupled to the ionization of internal groups in proteins: a self-guided Langevin dynamics study

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3220190

pKa of residue 66 in Staphylococal nuclease. I. Insights from QM/MM simulations with conventional sampling.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3220190

Electrostatic effects in a network of polar and ionizable groups in staphylococcal nuclease

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3220190

Calculating pH and salt dependence of protein-protein binding

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3220190

A buried lysine that titrates with a normal pKa: Role of conformational flexibility at the protein-water interface as a determinant of pKavalues

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3220190

Modeling electrostatic effects in proteins

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3220190

Benchmarking pK(a) prediction.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3220190

PPD v1.0--an integrated, web-accessible database of experimentally determined protein pKa values

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3220190

Biomolecular simulations at constant pH.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3220190

Reorganization in apo- and holo-beta-lactoglobulin upon protonation of Glu89: molecular dynamics and pKa calculations

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3220190

Site-specific contributions to the pH dependence of protein stability

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3220190

Electrostatic interactions.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3220190

Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3220190

Experimental pK(a) values of buried residues: analysis with continuum methods and role of water penetration

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3220190

What are the dielectric "constants" of proteins and how to validate electrostatic models?

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3220190

Simplified methods for pKa and acid pH-dependent stability estimation in proteins: removing dielectric and counterion boundaries.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3220190

Prediction of pH-dependent properties of proteins

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3220190

Benchmarking pKa Prediction Methods for Residues in Proteins.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3220190

On-the-path random walk sampling for efficient optimization of minimum free-energy path.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3220190

Essential energy space random walks to accelerate molecular dynamics simulations: convergence improvements via an adaptive-length self-healing strategy

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3220190

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

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3220190

Using a charging coordinate in studies of ionization induced partial unfolding

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3220190

Constant-pH molecular dynamics with ionic strength effects: protonation-conformation coupling in decalysine.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3220190

Constant pH molecular dynamics in generalized Born implicit solvent

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3220190

Improved pKa calculations through flexibility based sampling of a water-dominated interaction scheme.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3220190

pH-dependent stability and folding kinetics of a protein with an unusual alpha-beta topology: the C-terminal domain of the ribosomal protein L9.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3220190

The determinants of pKas in proteins

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3220190

Semianalytical treatment of solvation for molecular mechanics and dynamics

26 September 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23097

On the simulated scaling based free energy simulations: Adaptive optimization of the scaling parameter intervals.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23097

Energy difference space random walk to achieve fast free energy calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23097

A divide-and-conquer strategy to improve diffusion sampling in generalized ensemble simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23097

High tolerance for ionizable residues in the hydrophobic interior of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23097

Charges in the hydrophobic interior of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23097

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23097

Molecular simulation with variable protonation states at constant pH

21 January 2018

1 reference

12 December 2020

pH dependence of stability of staphylococcal nuclease: evidence of substantial electrostatic interactions in the denatured state

1 reference

12 December 2020

Dissociation and unfolding of bovine odorant binding protein at acidic pH

1 reference

12 December 2020

Role of the charge-charge interactions in defining stability and halophilicity of the CspB proteins

1 reference

12 December 2020

Identifiers

DOI

10.1002/PROT.23097

1 reference

8 August 2017

1 reference

8 August 2017

1 reference