Prediction of amphipathic in-plane membrane anchors in monotopic proteins using a SVM classifier.

ABSTRACT:

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

SUBMITTER: Sapay N 

PROVIDER: S-EPMC1564421 | biostudies-literature | 2006 May

REPOSITORIES: biostudies-literature