Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins (Q33239004)

24 July 2017

title

Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins (English)

1 reference

24 July 2017

main subject

transmembrane protein

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0 references

Pantelis G Bagos

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Stavros J Hamodrakas

1 reference

24 July 2017

author name string

Theodore D Liakopoulos

series ordinal

1 reference

24 July 2017

publication date

5 April 2006

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24 July 2017

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24 July 2017

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24 July 2017

page(s)

189

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describes a project that uses

24 July 2017

Bayes' theorem

1 reference

18 June 2022

https://europepmc.org/article/PMC/1523218

inferred from PubMed Central ID database lookup

cites work

A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

Improved membrane protein topology prediction by domain assignments

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

Global topology analysis of the Escherichia coli inner membrane proteome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

Evaluation of methods for predicting the topology of beta-barrel outer membrane proteins and a consensus prediction method

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

The Universal Protein Resource (UniProt)

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

A periplasmic fluorescent reporter protein and its application in high-throughput membrane protein topology analysis.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

PRED-TMBB: a web server for predicting the topology of beta-barrel outer membrane proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

ConPred II: a consensus prediction method for obtaining transmembrane topology models with high reliability.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

A combined transmembrane topology and signal peptide prediction method

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

A Hidden Markov Model method, capable of predicting and discriminating beta-barrel outer membrane proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

Prediction of lipoprotein signal peptides in Gram-negative bacteria

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

An ENSEMBLE machine learning approach for the prediction of all-alpha membrane proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

Topology models for 37 Saccharomyces cerevisiae membrane proteins based on C-terminal reporter fusions and predictions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

Crystal structure of bacterial multidrug efflux transporter AcrB

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

21 June 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=1523218

Rapid topology mapping of Escherichia coli inner-membrane proteins by prediction and PhoA/GFP fusion analysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

The HMMTOP transmembrane topology prediction server

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

CoPreTHi: a Web tool which combines transmembrane protein segment prediction methods.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

Evaluation of methods for the prediction of membrane spanning regions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

Probing protein surface topology by chemical surface labeling, crosslinking, and mass spectrometry

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

Assessing the accuracy of prediction algorithms for classification: an overview

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

Membrane topology and insertion of membrane proteins: search for topogenic signals

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

Determining the structure and mechanism of the human multidrug resistance P-glycoprotein using cysteine-scanning mutagenesis and thiol-modification techniques

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

JPred: a consensus secondary structure prediction server

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

Profile hidden Markov models

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

Principles governing amino acid composition of integral membrane proteins: application to topology prediction

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

Topology prediction for helical transmembrane proteins at 86% accuracy

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

Antibodies as tools to study the structure of membrane proteins: the case of the nicotinic acetylcholine receptor

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

The topological analysis of integral cytoplasmic membrane proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

A hidden Markov model that finds genes in E. coli DNA

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

TopPred II: an improved software for membrane protein structure predictions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

Beta-lactamase as a probe of membrane protein assembly and protein export

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

Analysis of membrane protein topology using alkaline phosphatase and beta-galactosidase gene fusions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

An HMM posterior decoder for sequence feature prediction that includes homology information

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

A hidden Markov model with molecular mechanics energy-scoring function for transmembrane helix prediction.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

Experimentally based topology models for E. coli inner membrane proteins

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

Predicting the topology of transmembrane helical proteins using mean burial propensity and a hidden-Markov-model-based method

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

Reliability measures for membrane protein topology prediction algorithms.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

MaxSubSeq: an algorithm for segment-length optimization. The case study of the transmembrane spanning segments

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

Membrane topology of a multidrug efflux transporter, AcrB, in Escherichia coli

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

Prediction of signal peptides and signal anchors by a hidden Markov model.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

Two methods for improving performance of an HMM and their application for gene finding

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

Prediction of protein secondary structure by the hidden Markov model.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

Multiple alignment using hidden Markov models

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523218

Consensus predictions of membrane protein topology

31 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16597327

12 December 2020

inferred from PubMed ID database lookup

Refining neural network predictions for helical transmembrane proteins by dynamic programming

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16597327

12 December 2020

inferred from PubMed ID database lookup

The presence of signal peptide significantly affects transmembrane topology prediction

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16597327

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1186/1471-2105-7-189

1 reference

24 July 2017

DBLP publication ID

journals/bmcbi/BagosLH06

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

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1 reference

24 July 2017

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