(Q34824981)

4 August 2017

Engineering a more thermostable blue light photo receptor Bacillus subtilis YtvA LOV domain by a computer aided rational design method (English)

1 reference

4 August 2017

1 reference

6

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author name string

Xiangfei Song

1

1 reference

4 August 2017

Yefei Wang

2

1 reference

4 August 2017

Zhiyu Shu

3

1 reference

4 August 2017

Jingbo Hong

4

1 reference

4 August 2017

Tong Li

5

1 reference

4 August 2017

4 July 2013

1 reference

PLOS Computational Biology

4 August 2017

1 reference

4 August 2017

9

1 reference

4 August 2017

e1003129

1 reference

4 August 2017

7

1 reference

Creative Commons Attribution 4.0 International

4 August 2017

start time

4 July 2013

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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

1 reference

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Soft-core potentials in thermodynamic integration: comparing one- and two-step transformations

8 July 2018

1 reference

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Role of conformational sampling in computing mutation-induced changes in protein structure and stability

8 July 2018

1 reference

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ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules

8 July 2018

1 reference

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Flavin mononucleotide-based fluorescent reporter proteins outperform green fluorescent protein-like proteins as quantitative in vivo real-time reporters

8 July 2018

1 reference

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Protein thermostability calculations using alchemical free energy simulations

8 July 2018

1 reference

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Rational stabilization of enzymes by computational redesign of surface charge-charge interactions

8 July 2018

1 reference

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Structural Basis for Light-dependent Signaling in the Dimeric LOV Domain of the Photosensor YtvA

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3701716

High-resolution structural and thermodynamic analysis of extreme stabilization of human procarboxypeptidase by computational protein design

8 July 2018

1 reference

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GROMACS: fast, flexible, and free

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3701716

Initial characterization of a blue-light sensing, phototropin-related protein from Pseudomonas putida: a paradigm for an extended LOV construct

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3701716

I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3701716

Energy functions for protein design: adjustment with protein-protein complex affinities, models for the unfolded state, and negative design of solubility and specificity.

8 July 2018

1 reference

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A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6

8 July 2018

1 reference

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Repacking the Core of T4 lysozyme by automated design

8 July 2018

1 reference

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Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations

8 July 2018

1 reference

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First evidence for phototropin-related blue-light receptors in prokaryotes

8 July 2018

1 reference

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Directed evolution of a thermostable esterase.

8 July 2018

1 reference

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Dependence of protein stability on the structure of the denatured state: free energy calculations of I56V mutation in human lysozyme

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3701716

Probing the role of packing specificity in protein design

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3701716

Green fluorescent protein as a marker for gene expression

8 July 2018

1 reference

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Energetic cost and structural consequences of burying a hydroxyl group within the core of a protein determined from Ala-->Ser and Val-->Thr substitutions in T4 lysozyme

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3701716

Effect of cavity-creating mutations in the hydrophobic core of chymotrypsin inhibitor 2

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3701716

Wavelength mutations and posttranslational autoxidation of green fluorescent protein

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3701716

Decomposition of interaction free energies in proteins and other complex systems.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3701716

Free energy via molecular simulation: applications to chemical and biomolecular systems

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3701716

Basic local alignment search tool

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3701716

On the interpretation of biochemical data by molecular dynamics computer simulation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3701716

A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3701716

Contribution of surface salt bridges to protein stability: guidelines for protein engineering.

8 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003129

A computational approach for the rational design of stable proteins and enzymes: optimization of surface charge-charge interactions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003129

Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003129

Reporter proteins for in vivo fluorescence without oxygen.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003129

The missing term in effective pair potentials

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003129

The meaning of component analysis: decomposition of the free energy in terms of specific interactions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003129

Subunit interactions provide a significant contribution to the stability of the dimeric four-alpha-helical-bundle protein ROP.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003129

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003129

Sequence statistics reliably predict stabilizing mutations in a protein domain

21 January 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3701716

26 October 2018

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003129

Decomposition of the Free Energy of a System in Terms of Specific Interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003129

Protein stabilization by removal of unsatisfied polar groups: computational approaches and experimental tests

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23861663

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Predicting free energy changes using structural ensembles

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23861663

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Striking stabilization of Arc repressor by an engineered disulfide bond

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23861663

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PCBI.1003129

1 reference

journals/ploscb/SongWSHLY13

4 August 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

4 August 2017

1 reference