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Prediction of amphipathic in-plane membrane anchors in monotopic proteins using a SVM classifier
BACKGROUND: Membrane proteins are estimated to represent about 25% of open reading frames in fully sequenced genomes. However, the experimental study of proteins remains difficult. Considerable efforts have thus been made to develop prediction methods. Most of these were conceived to detect transmem...
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2006
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1564421/ https://www.ncbi.nlm.nih.gov/pubmed/16704727 http://dx.doi.org/10.1186/1471-2105-7-255 |
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author | Sapay, Nicolas Guermeur, Yann Deléage, Gilbert |
author_facet | Sapay, Nicolas Guermeur, Yann Deléage, Gilbert |
author_sort | Sapay, Nicolas |
collection | PubMed |
description | BACKGROUND: Membrane proteins are estimated to represent about 25% of open reading frames in fully sequenced genomes. However, the experimental study of proteins remains difficult. Considerable efforts have thus been made to develop prediction methods. Most of these were conceived to detect transmembrane helices in polytopic proteins. Alternatively, a membrane protein can be monotopic and anchored via an amphipathic helix inserted in a parallel way to the membrane interface, so-called in-plane membrane (IPM) anchors. This type of membrane anchor is still poorly understood and no suitable prediction method is currently available. RESULTS: We report here the "AmphipaSeeK" method developed to predict IPM anchors. It uses a set of 21 reported examples of IPM anchored proteins. The method is based on a pattern recognition Support Vector Machine with a dedicated kernel. CONCLUSION: AmphipaSeeK was shown to be highly specific, in contrast with classically used methods (e.g. hydrophobic moment). Additionally, it has been able to retrieve IPM anchors in naively tested sets of transmembrane proteins (e.g. PagP). AmphipaSeek and the list of the 21 IPM anchored proteins is available on NPS@, our protein sequence analysis server. |
format | Text |
id | pubmed-1564421 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2006 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-15644212006-09-14 Prediction of amphipathic in-plane membrane anchors in monotopic proteins using a SVM classifier Sapay, Nicolas Guermeur, Yann Deléage, Gilbert BMC Bioinformatics Methodology Article BACKGROUND: Membrane proteins are estimated to represent about 25% of open reading frames in fully sequenced genomes. However, the experimental study of proteins remains difficult. Considerable efforts have thus been made to develop prediction methods. Most of these were conceived to detect transmembrane helices in polytopic proteins. Alternatively, a membrane protein can be monotopic and anchored via an amphipathic helix inserted in a parallel way to the membrane interface, so-called in-plane membrane (IPM) anchors. This type of membrane anchor is still poorly understood and no suitable prediction method is currently available. RESULTS: We report here the "AmphipaSeeK" method developed to predict IPM anchors. It uses a set of 21 reported examples of IPM anchored proteins. The method is based on a pattern recognition Support Vector Machine with a dedicated kernel. CONCLUSION: AmphipaSeeK was shown to be highly specific, in contrast with classically used methods (e.g. hydrophobic moment). Additionally, it has been able to retrieve IPM anchors in naively tested sets of transmembrane proteins (e.g. PagP). AmphipaSeek and the list of the 21 IPM anchored proteins is available on NPS@, our protein sequence analysis server. BioMed Central 2006-05-16 /pmc/articles/PMC1564421/ /pubmed/16704727 http://dx.doi.org/10.1186/1471-2105-7-255 Text en Copyright © 2006 Sapay et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Methodology Article Sapay, Nicolas Guermeur, Yann Deléage, Gilbert Prediction of amphipathic in-plane membrane anchors in monotopic proteins using a SVM classifier |
title | Prediction of amphipathic in-plane membrane anchors in monotopic proteins using a SVM classifier |
title_full | Prediction of amphipathic in-plane membrane anchors in monotopic proteins using a SVM classifier |
title_fullStr | Prediction of amphipathic in-plane membrane anchors in monotopic proteins using a SVM classifier |
title_full_unstemmed | Prediction of amphipathic in-plane membrane anchors in monotopic proteins using a SVM classifier |
title_short | Prediction of amphipathic in-plane membrane anchors in monotopic proteins using a SVM classifier |
title_sort | prediction of amphipathic in-plane membrane anchors in monotopic proteins using a svm classifier |
topic | Methodology Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1564421/ https://www.ncbi.nlm.nih.gov/pubmed/16704727 http://dx.doi.org/10.1186/1471-2105-7-255 |
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