(Q34727787)

4 August 2017

title

Analysis of the peroxiredoxin family: using active-site structure and sequence information for global classification and residue analysis (English)

1 reference

4 August 2017

6

1 reference

4 August 2017

Laura Soito

3

0 references

Leslie B Poole

object named as

Leslie B Poole

5

0 references

author name string

Kimberly J Nelson

1

1 reference

4 August 2017

Stacy T Knutson

2

1 reference

4 August 2017

Chananat Klomsiri

4

1 reference

4 August 2017

language of work or name

English

0 references

publication date

22 December 2010

1 reference

4 August 2017

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4 August 2017

volume

79

1 reference

4 August 2017

issue

3

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4 August 2017

page(s)

947-964

1 reference

PREX: PeroxiRedoxin classification indEX, a database of subfamily assignments across the diverse peroxiredoxin family

4 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=3065352

Structure-based insights into the catalytic power and conformational dexterity of peroxiredoxins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Structural Evidence that Peroxiredoxin Catalytic Power Is Based on Transition-State Stabilization

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Conformational and oligomeric effects on the cysteine pK(a) of tryparedoxin peroxidase

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

High quality protein sequence alignment by combining structural profile prediction and profile alignment using SABER-TOOTH.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Annotation error in public databases: misannotation of molecular function in enzyme superfamilies

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Insights into the alkyl peroxide reduction pathway of Xanthomonas campestris bacterioferritin comigratory protein from the trapped intermediate-ligand complex structures

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Typical 2-Cys peroxiredoxins--structures, mechanisms and functions.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Prediction of membrane-protein topology from first principles

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Active site profiling to identify protein functional sites in sequences and structures using the Deacon Active Site Profiler (DASP).

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Reconciling the chemistry and biology of reactive oxygen species

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Redox control in trypanosomatids, parasitic protozoa with trypanothione-based thiol metabolism

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

ConFunc--functional annotation in the twilight zone

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

The catalytic mechanism of peroxiredoxins.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Clustal W and Clustal X version 2.0

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Exploring inconsistencies in genome-wide protein function annotations: a machine learning approach

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Estimating the annotation error rate of curated GO database sequence annotations

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Four thiol peroxidases contain a conserved GCT catalytic motif and act as a versatile array of lipid peroxidases in Anabaena sp. PCC7120.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Hydrogen peroxide sensing and signaling

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Oxidation state governs structural transitions in peroxiredoxin II that correlate with cell cycle arrest and recovery

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Analysis of the link between enzymatic activity and oligomeric state in AhpC, a bacterial peroxiredoxin

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

The plant multigenic family of thiol peroxidases

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Contribution of the Helicobacter pylori thiol peroxidase bacterioferritin comigratory protein to oxidative stress resistance and host colonization

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

eBLOCKs: enumerating conserved protein blocks to achieve maximal sensitivity and specificity

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Bacterial defenses against oxidants: mechanistic features of cysteine-based peroxidases and their flavoprotein reductases

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Divergence of function in the thioredoxin fold suprafamily: evidence for evolution of peroxiredoxins from a thioredoxin-like ancestor

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Enzyme-specific profiles for genome annotation: PRIAM

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Essential role for the peroxiredoxin Prdx1 in erythrocyte antioxidant defence and tumour suppression

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

The mechanism of Mycobacterium tuberculosis alkylhydroperoxidase AhpD as defined by mutagenesis, crystallography, and kinetics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Peroxiredoxin evolution and the regulation of hydrogen peroxide signaling

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Peroxiredoxin II is essential for sustaining life span of erythrocytes in mice.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

The tetrameric structure of Haemophilus influenza hybrid Prx5 reveals interactions between electron donor and acceptor proteins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Structure, mechanism and regulation of peroxiredoxins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Metabolic enzymes of mycobacteria linked to antioxidant defense by a thioredoxin-like protein

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

A motif-based profile scanning approach for genome-wide prediction of signaling pathways

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Thioredoxin-dependent hydroperoxide peroxidase activity of bacterioferritin comigratory protein (BCP) as a new member of the thiol-specific antioxidant protein (TSA)/Alkyl hydroperoxide peroxidase C (AhpC) family

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

7 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=3065352

Recognition of spatial motifs in protein structures

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Methods and statistics for combining motif match scores

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Protein fold recognition by prediction-based threading

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Prediction and evaluation of side-chain conformations for protein backbone structures

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Go hunting in sequence databases but watch out for the traps

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Prediction of protein structure by evaluation of sequence-structure fitness. Aligning sequences to contact profiles derived from three-dimensional structures

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Cloning and sequencing of thiol-specific antioxidant from mammalian brain: alkyl hydroperoxide reductase and thiol-specific antioxidant define a large family of antioxidant enzymes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

PRINTS--a database of protein motif fingerprints.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

A quantitative methodology for the de novo design of proteins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Profile analysis: detection of distantly related proteins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

PROSITE: a dictionary of sites and patterns in proteins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Exhaustive matching of the entire protein sequence database

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065352

Identity and functions of CxxC-derived motifs

7 July 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22936

Crystal structure of an archaeal peroxiredoxin from the aerobic hyperthermophilic crenarchaeon Aeropyrum pernix K1.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22936

Crystal structure of a novel Plasmodium falciparum 1-Cys peroxiredoxin

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22936

The difficulty of annotating genes: the case of putrescine carbamoyltransferase

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22936

Whole-genome sequence annotation: 'Going wrong with confidence'.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22936

Structure-based Active Site Profiles for Genome Analysis and Functional Family Subclassification

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22936

Synergistic computational and experimental proteomics approaches for more accurate detection of active serine hydrolases in yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22936

Poplar peroxiredoxin Q. A thioredoxin-linked chloroplast antioxidant functional in pathogen defense

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22936

Characterization of the yeast peroxiredoxin Ahp1 in its reduced active and overoxidized inactive forms using NMR.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22936

Thioredoxin-linked "thiol peroxidase" from periplasmic space of Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22936

Dimers to doughnuts: redox-sensitive oligomerization of 2-cysteine peroxiredoxins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22936

Structure and mechanism of the alkyl hydroperoxidase AhpC, a key element of the Mycobacterium tuberculosis defense system against oxidative stress

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22936

An NADH-dependent bacterial thioredoxin reductase-like protein in conjunction with a glutaredoxin homologue form a unique peroxiredoxin (AhpC) reducing system in Clostridium pasteurianum.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22936

Preference functions for prediction of membrane-buried helices in integral membrane proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22936

Blocks+: a non-redundant database of protein alignment blocks derived from multiple compilations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22936

'Going wrong with confidence': misleading sequence analyses of CiaB and ClpX

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22936

Chemical and Structural Diversity in Cyclooxygenase Protein Active Sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22936

Editorial Commentary: Trichomonas vaginalisInfection: The Most Prevalent Nonviral Sexually Transmitted Infection Receives the Least Public Health Attention

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22936

An approach to improving multiple alignments of protein sequences using predicted secondary structure

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21287625

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

What we do not know about sequence analysis and sequence databases

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21287625

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The high reactivity of peroxiredoxin 2 with H(2)O(2) is not reflected in its reaction with other oxidants and thiol reagents

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21287625

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/PROT.22936

1 reference

4 August 2017

1 reference

4 August 2017

1 reference