(Q51501233)

6 April 2018

title

Exploring conformational changes coupled to ionization states using a hybrid Rosetta-MCCE protocol. (English)

1 reference

6 April 2018

author name string

Yifan Song

series ordinal

1

1 reference

6 April 2018

language of work or name

English

0 references

publication date

30 August 2011

1 reference

6 April 2018

published in

Proteins

1 reference

6 April 2018

volume

79

1 reference

6 April 2018

issue

12

1 reference

6 April 2018

page(s)

3356-3363

1 reference

6 April 2018

Benchmarking pK(a) prediction.

cites work

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23146

Benchmarking pKa Prediction Methods for Residues in Proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23146

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23146

Are acidic and basic groups in buried proteins predicted to be ionized?

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23146

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.23146

Use of 1H NMR spectroscopy and computer simulations To analyze histidine pKa changes in a protein tyrosine phosphatase: experimental and theoretical determination of electrostatic properties in a small protein.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23146

Molecular dynamics study of water penetration in staphylococcal nuclease.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23146

Towards a quantitative understanding of protein hydration and volumetric properties

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23146

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23146

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23146

MCCE analysis of the pKas of introduced buried acids and bases in staphylococcal nuclease.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23146

Developing hybrid approaches to predict pKa values of ionizable groups

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23146

Protein structure prediction using Rosetta

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23146

Progress in modeling of protein structures and interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23146

Calculated protein and proton motions coupled to electron transfer: electron transfer from QA- to QB in bacterial photosynthetic reaction centers.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23146

Effective energy function for proteins in solution

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23146

Improved prediction of protein side-chain conformations with SCWRL4

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23146

Rotamer libraries in the 21st century

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23146

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23146

CHARMM: the biomolecular simulation program

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23146

An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23146

The crystal structure of staphylococcal nuclease refined at 1.7 A resolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23146

Equation of State Calculations by Fast Computing Machines

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23146

Conformational consequences of ionization of Lys, Asp, and Glu buried at position 66 in staphylococcal nuclease

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23146

Charges in the hydrophobic interior of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23146

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.23146

Arginine residues at internal positions in a protein are always charged

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23146

Protein electrostatics and pKa blind predictions; contribution from empirical predictions of internal ionizable residues.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23146

Backbone dipoles generate positive potentials in all proteins: origins and implications of the effect

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23146

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23146

21 January 2018

Identifiers

DOI

10.1002/PROT.23146

1 reference

6 April 2018

1 reference

6 April 2018