Prediction of the transmembrane regions of beta-barrel membrane proteins with a neural network-based predictor (Q30168358)

1 September 2017

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

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artificial neural network

1 September 2017

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transmembrane protein

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1 September 2017

I Jacoboni

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1 September 2017

P L Martelli

series ordinal

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1 September 2017

P Fariselli

series ordinal

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1 September 2017

R Casadio

series ordinal

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1 September 2017

1 April 2001

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1 September 2017

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1 September 2017

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1 September 2017

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1 September 2017

779-787

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describes a project that uses

1 September 2017

artificial neural network

1 reference

based on heuristic

inferred from title

cites work

Crystal structure of Omp32, the anion-selective porin from Comamonas acidovorans, in complex with a periplasmic peptide at 2.1 A resolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

beta-Barrel membrane proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

Crystal structure of the bacterial membrane protein TolC central to multidrug efflux and protein export

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

Application of multiple sequence alignment profiles to improve protein secondary structure prediction

3 June 2018

1 reference

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The structure of the outer membrane protein OmpX from Escherichia coli reveals possible mechanisms of virulence

3 June 2018

1 reference

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Structural evidence for dimerization-regulated activation of an integral membrane phospholipase

3 June 2018

1 reference

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Analysis and assessment of ab initio three-dimensional prediction, secondary structure, and contacts prediction

3 June 2018

1 reference

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Addressing the issue of sequence-to-structure alignments in comparative modeling of CASP3 target proteins.

3 June 2018

1 reference

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Membrane protein folding and stability: physical principles

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

Progress in protein structure prediction: assessment of CASP3.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

Crystal structure of the outer membrane active transporter FepA from Escherichia coli

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

Siderophore-mediated iron transport: crystal structure of FhuA with bound lipopolysaccharide

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

Prediction by a neural network of outer membrane beta-strand protein topology

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

Structure of the outer membrane protein A transmembrane domain

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

Conformational changes in the mitochondrial channel protein, VDAC, and their functional implications

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

The HSSP database of protein structure-sequence alignments and family profiles

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

Identification of membrane spanning beta strands in bacterial porins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

Structure of maltoporin from Salmonella typhimurium ligated with a nitrophenyl-maltotrioside

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

Structure of staphylococcal alpha-hemolysin, a heptameric transmembrane pore

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

A predictor of transmembrane alpha-helix domains of proteins based on neural networks.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

Topology prediction for helical transmembrane proteins at 86% accuracy

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

Porins: general to specific, native to engineered passive pores

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

An alternative topological model for Escherichia coli OmpA.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

The structure of OmpF porin in a tetragonal crystal form

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

Transbilayer pores formed by beta-barrels: molecular modeling of pore structures and properties

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

Gibbs motif sampling: detection of bacterial outer membrane protein repeats

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

Prediction of membrane-spanning beta-strands and its application to maltoporin

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

Folding pattern diversity of integral membrane proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

A model recognition approach to the prediction of all-helical membrane protein structure and topology

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

Transmembrane helices predicted at 95% accuracy

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

Refined structure of the porin from Rhodopseudomonas blastica. Comparison with the porin from Rhodobacter capsulatus

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

A general method applicable to the search for similarities in the amino acid sequence of two proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

Folding patterns of porin and bacteriorhodopsin.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

Basic local alignment search tool

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

Database of homology-derived protein structures and the structural meaning of sequence alignment

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

Prediction of the general structure of OmpF and PhoE from the sequence and structure of porin from Rhodobacter capsulatus. Orientation of porin in the membrane

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

Structure of porin refined at 1.8 A resolution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

An optimization approach to predicting protein structural class from amino acid composition

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373968

3 June 2018

1 reference

https://pubmed.ncbi.nlm.nih.gov/11274469

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1110/PS.37201

1 reference

1 September 2017

1 reference

1 September 2017

PubMed publication ID

11274469

1 reference