Predicting transmembrane beta-barrels in proteomes (Q30164081)

24 September 2017

Predicting transmembrane beta-barrels in proteomes (English)

1 reference

24 September 2017

0 references

transmembrane protein

0 references

author

Jinfeng Liu

series ordinal

3

1 reference

24 September 2017

5

Burkhard Rost

1 reference

24 September 2017

4

Dariusz Przybylski

1 reference

24 September 2017

Henry R Bigelow

1

1 reference

PMCID

419468

24 September 2017

Donald S Petrey

series ordinal

2

1 reference

PMCID

419468

24 September 2017

language of work or name

English

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publication date

11 May 2004

1 reference

24 September 2017

Nucleic Acids Research

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24 September 2017

32

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24 September 2017

8

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24 September 2017

2566-2577

1 reference

State-of-the-art in membrane protein prediction

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=419468

The structure of a mycobacterial outer-membrane channel

3 June 2018

1 reference

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GRASP2: visualization, surface properties, and electrostatics of macromolecular structures and sequences

3 June 2018

1 reference

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3 June 2018

1 reference

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The versatile beta-barrel membrane protein

3 June 2018

1 reference

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Mycobacterial porins--new channel proteins in unique outer membranes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=419468

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3 June 2018

1 reference

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The PredictProtein server.

3 June 2018

1 reference

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A HMM-based method to predict the transmembrane regions of beta-barrel membrane proteins

3 June 2018

1 reference

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3 June 2018

1 reference

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3 June 2018

1 reference

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PEP: Predictions for Entire Proteomes

3 June 2018

1 reference

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1 reference

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3 June 2018

1 reference

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Structure and dynamics of the beta-barrel of the membrane transporter BtuB by site-directed spin labeling

3 June 2018

1 reference

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The beta-barrel finder (BBF) program, allowing identification of outer membrane beta-barrel proteins encoded within prokaryotic genomes

3 June 2018

1 reference

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A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins

3 June 2018

1 reference

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3 June 2018

1 reference

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3 June 2018

1 reference

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3 June 2018

1 reference

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3 June 2018

1 reference

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Toward genomic identification of beta-barrel membrane proteins: composition and architecture of known structures

3 June 2018

1 reference

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Predicting protein conformation by statistical methods.

3 June 2018

1 reference

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3 June 2018

1 reference

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Review: protein secondary structure prediction continues to rise.

3 June 2018

1 reference

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Review: prediction of in vivo fates of proteins in the era of genomics and proteomics

3 June 2018

1 reference

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3 June 2018

1 reference

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3 June 2018

1 reference

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Prediction of the transmembrane regions of beta-barrel membrane proteins with a neural network-based predictor

3 June 2018

1 reference

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3 June 2018

1 reference

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3 June 2018

1 reference

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Bacterial phospholipase A: structure and function of an integral membrane phospholipase

3 June 2018

1 reference

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beta-Barrel membrane proteins

3 June 2018

1 reference

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Structure and function of bacterial outer membrane proteins: barrels in a nutshell

3 June 2018

1 reference

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3 June 2018

1 reference

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3 June 2018

1 reference

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The Protein Data Bank

1 reference

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3 June 2018

1 reference

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3 June 2018

1 reference

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3 June 2018

1 reference

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3 June 2018

1 reference

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3 June 2018

1 reference

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Twilight zone of protein sequence alignments

3 June 2018

1 reference

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A modified definition of Sov, a segment-based measure for protein secondary structure prediction assessment.

3 June 2018

1 reference

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3 June 2018

1 reference

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3 June 2018

1 reference

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3 June 2018

1 reference

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3 June 2018

1 reference

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3 June 2018

1 reference

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3 June 2018

1 reference

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3 June 2018

1 reference

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1 reference

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1 reference

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3 June 2018

1 reference

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1 reference

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3 June 2018

1 reference

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3 June 2018

1 reference

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3 June 2018

1 reference

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3 June 2018

1 reference

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1 reference

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1 reference

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3 June 2018

1 reference

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1 reference

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3 June 2018

1 reference

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3 June 2018

1 reference

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3 June 2018

1 reference

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Identifiers

DOI

10.1093/NAR/GKH580

1 reference

24 September 2017

1 reference

24 September 2017

1 reference

PMCID

419468