Transmembrane protein topology prediction using support vector machines (Q33452897)

26 July 2017

Transmembrane protein topology prediction using support vector machines (English)

1 reference

26 July 2017

transmembrane protein

0 references

support vector machine

1 reference

2

David T Jones

1 reference

26 July 2017

Timothy Nugent

1

1 reference

26 July 2017

26 May 2009

1 reference

26 July 2017

1 reference

26 July 2017

10

1 reference

26 July 2017

159

1 reference

Creative Commons Attribution 2.0 Generic

26 July 2017

start time

26 May 2009

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

1 reference

April 2022 Public Data File from Crossref

describes a project that uses

support vector machine

1 reference

based on heuristic

inferred from title

exact match

https://scigraph.springernature.com/pub.10.1186/1471-2105-10-159

0 references

cites work

SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700806

OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700806

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700806

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700806

TOPDB: topology data bank of transmembrane 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=2700806

Membrane protein structural biology--how far can the bugs take us?

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700806

Locating proteins in the cell using TargetP, SignalP and related tools

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700806

Improving the accuracy of transmembrane protein topology prediction using evolutionary 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=2700806

PONGO: a web server for multiple predictions of all-alpha transmembrane 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=2700806

Algorithms for incorporating prior topological information in HMMs: application to transmembrane 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=2700806

OPM: orientations of proteins in membranes database

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700806

Pufferfish and zebrafish have five distinct NPY receptor subtypes, but have lost appetite receptors Y1 and Y5.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700806

PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700806

Improved prediction of signal peptides: SignalP 3.0

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700806

The progress of membrane protein structure determination

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700806

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=2700806

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=2700806

Transmembrane protein domains rarely use covalent domain recombination as an evolutionary mechanism

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700806

Two motifs target Batten disease protein CLN3 to lysosomes in transfected nonneuronal and neuronal cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700806

Announcing the worldwide Protein Data Bank

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700806

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=2700806

Membrane topology of CLN3, the protein underlying Batten disease

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700806

The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700806

Transmembrane helix predictions revisited

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700806

Genomic analysis of membrane protein families: abundance and conserved motifs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700806

Improved detection of homologous membrane proteins by inclusion of information from topology 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=2700806

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=2700806

PRED-CLASS: cascading neural networks for generalized protein classification and genome-wide applications

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700806

MPtopo: A database of membrane protein 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=2700806

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=2700806

SOSUI: classification and secondary structure prediction system for 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=2700806

Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700806

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700806

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=2700806

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=2700806

Patterns of amino acids near signal-sequence cleavage sites

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700806

A putative signal peptidase recognition site and sequence in eukaryotic and prokaryotic signal peptides

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700806

Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700806

Comparison of the predicted and observed secondary structure of T4 phage lysozyme

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700806

A combinatorial pattern discovery approach for the prediction of membrane dipping (re-entrant) loops.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700806

Structural classification and prediction of reentrant regions in alpha-helical transmembrane proteins: application to complete genomes.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700806

An HMM posterior decoder for sequence feature prediction that includes homology 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=2700806

Transmembrane helix prediction: a comparative evaluation and analysis.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700806

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=2700806

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=2700806

A collection of well characterised integral 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=2700806

Comparative genomics of the human and Fugu voltage-gated calcium channel α1-subunit gene family reveals greater diversity in Fugu

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700806

Enhanced membrane protein topology prediction using a hierarchical classification method and a new scoring function.

31 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19470175

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Topological rules for membrane protein assembly in eukaryotic cells

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19470175

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2105-10-159

1 reference

26 July 2017

journals/bmcbi/NugentJ09

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

26 July 2017

1 reference

PubMed ID

19470175