(Q34168395)

31 July 2017

title

Deciphering the preference and predicting the viability of circular permutations in proteins (English)

1 reference

circular permutation in proteins

31 July 2017

main subject

0 references

author name string

Wei-Cheng Lo

1

1 reference

31 July 2017

Tian Dai

2

1 reference

31 July 2017

Yen-Yi Liu

3

1 reference

31 July 2017

Li-Fen Wang

4

1 reference

31 July 2017

Jenn-Kang Hwang

5

1 reference

31 July 2017

Ping-Chiang Lyu

6

1 reference

31 July 2017

language of work or name

English

0 references

publication date

16 February 2012

1 reference

31 July 2017

1 reference

31 July 2017

volume

7

1 reference

31 July 2017

issue

2

1 reference

31 July 2017

page(s)

e31791

1 reference

Creative Commons Attribution 4.0 International

31 July 2017

copyright license

start time

16 February 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Circular permutation: a different way to engineer enzyme structure and function

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

GIS: a comprehensive source for protein structure similarities

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Determination of ensemble-average pairwise root mean-square deviation from experimental B-factors.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

The folding, stability and conformational dynamics of beta-barrel fluorescent proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Context-independent, temperature-dependent helical propensities for amino acid residues

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

In vivo and in vitro protein ligation by naturally occurring and engineered split DnaE inteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

CPDB: a database of circular permutation in proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Novel protein folds and their nonsequential structural analogs

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Deriving protein dynamical properties from weighted protein contact number.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

On the relationship between the protein structure and protein dynamics.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

CPSARST: an efficient circular permutation search tool applied to the detection of novel protein structural relationships

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Protein structural similarity search by Ramachandran codes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Duplication, divergence and formation of novel protein topologies

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Revealing divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Protein structure database search and evolutionary classification.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Protein ligation: an enabling technology for the biophysical analysis of proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Structural stabilization of GTP-binding domains in circularly permuted GTPases: implications for RNA binding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Favin versus concanavalin A: Circularly permuted amino acid sequences

5 July 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

5 July 2018

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031791

Engineering and characterization of a superfolder green fluorescent protein

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Identification and characterization of key substructures involved in the early folding events of a (beta/alpha)8-barrel protein as studied by experimental and computational methods.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

The Amber biomolecular simulation programs

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Importance of terminal residues on circularly permutated Escherichia coli alkaline phosphatase with high specific activity.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Improving the Catalytic Activity of Candida antarctica Lipase B by Circular Permutation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Engineering allosteric protein switches by domain insertion

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

TM-align: a protein structure alignment algorithm based on the TM-score

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Rapid motif-based prediction of circular permutations in multi-domain proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Prediction of protein relative solvent accessibility with a two-stage SVM approach.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

FAST: a novel protein structure alignment algorithm.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Circular permutation as a tool to reduce surface entropy triggers crystallization of the signal recognition particle receptor beta subunit

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Transition states for folding of circular-permuted proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Alteration of the disulfide-coupled folding pathway of BPTI by circular permutation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Crystal structure of a natural circularly permuted jellyroll protein: 1,3-1,4-beta-D-glucanase from Fibrobacter succinogenes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Atom depth as a descriptor of the protein interior

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Plasticity of enzyme active sites

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Dynamics of proteins in crystals: comparison of experiment with simple models

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Conformations of amino acids in proteins.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Prediction of coordination number and relative solvent accessibility in proteins.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Sequence permutations in the molecular evolution of DNA methyltransferases

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Flexibility and packing in proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Regulatory potential, phyletic distribution and evolution of ancient, intracellular small-molecule-binding domains.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Disulfide bond effects on protein stability: designed variants of Cucurbita maxima trypsin inhibitor-V.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Different circular permutations produced different folding nuclei in proteins: a computational study

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB)

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

A simple algorithm for detecting circular permutations in proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

5 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=3281007

Flexible sequence similarity searching with the FASTA3 program package

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Circular permutation and receptor insertion within green fluorescent proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Circularly permuted variants of the green fluorescent protein

5 July 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

5 July 2018

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031791

Circular Permutations in the Molecular Evolution of DNA Methyltransferases

21 January 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

5 July 2018

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031791

Random circular permutation of DsbA reveals segments that are essential for protein folding and stability

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Circular permutations of natural protein sequences: structural evidence

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Disulfide bonds and the stability of globular proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Early intermediates in the folding of dihydrofolate reductase from Escherichia coli detected by hydrogen exchange and NMR

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Swaposins: circular permutations within genes encoding saposin homologues

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Solvent-accessible surfaces of proteins and nucleic acids

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

The interpretation of protein structures: Estimation of static accessibility

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Polypeptide ligation occurs during post-translational modification of concanavalin A

5 July 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

5 July 2018

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031791

Suggestions for "safe" residue substitutions in site-directed mutagenesis.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Circular permutation and deletion studies of myoglobin indicate that the correct position of its N-terminus is required for native stability and solubility but not for native-like heme binding and folding.

5 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031791

Fancy footwork in the sequence space shuffle.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031791

Prediction of viable circular permutants using a graph theoretic approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031791

Amino acid coupling patterns in thermophilic proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031791

IMGT standardized criteria for statistical analysis of immunoglobulin V-REGION amino acid properties.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031791

A simple way to compute protein dynamics without a mechanical model.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031791

On the relation between residue flexibility and local solvent accessibility in proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031791

A unification of the elastic network model and the Gaussian network model for optimal description of protein conformational motions and fluctuations

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031791

Detection of protein-protein interactions using a simple survival protein-fragment complementation assay based on the enzyme dihydrofolate reductase.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031791

Gaussian Dynamics of Folded Proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031791

Evolution of new protein topologies through multistep gene rearrangements

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3281007

Network Analysis of Protein Structures Identifies Functional Residues

28 October 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031791

Highly efficient proteintrans-splicing by a naturally split DnaE intein fromNostoc punctiforme

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031791

Systematic circular permutation of an entire protein reveals essential folding elements

21 January 2018

1 reference

12 December 2020

Receiver operating characteristic (ROC) analysis: basic principles and applications in radiology

1 reference

12 December 2020

Sequence codes for extended conformation: a neighbor-dependent sequence analysis of loops in proteins

1 reference

12 December 2020

Side chain contributions to the stability of alpha-helical structure in peptides

1 reference

12 December 2020

Naturally occurring circular permutations in proteins

1 reference

12 December 2020

Circular permutation analysis as a method for distinction of functional elements in the M20 loop of Escherichia coli dihydrofolate reductase

1 reference

12 December 2020

Radial locations of amino acid residues in a globular protein: correlation with the sequence

1 reference

12 December 2020

Mapping the distribution of conformational information throughout a protein sequence

1 reference

12 December 2020

10.1371/JOURNAL.PONE.0031791

Identifiers

DOI

1 reference

31 July 2017

0 references

1 reference

31 July 2017

1 reference