AmphipaSeeK

Synopsis

AmphipaSeek is a prediction method of amphipathic in-plane membrane anchors (IPM anchors) in protein sequences. IPM anchors are a particular type of membrane segment found in monotopic proteins (e.g. NonStructural protein 5A of the Hepatitis C virus, the mammal Prostaglandin H2 Synthase) or in polytopic proteins (e.g. gp41 and Vpu of the Human Immunodeficiency Virus). AmphipaSeeK has been initally developed with a set of 21 monotopic membrane proteins with an experimentally characterized IPM anchor. The set is currently extended to IPM segments found in transmembrane proteins. To date, 7 transmembrane proteins has been added to the initial data set.

[ ! ] AmphipaSeeK is not a prediction method of transmembrane segments [ ! ]

Availability

AmphipaSeeK is availbale on the NPS@ web server : http://npsa-pbil.ibcp.fr/

Reference

If you use AmphipaSeeK in a publication, please cite :

Sapay N., Guermeur Y., and Deléage G (2005) Prediction of amphipathic in-plane membrane anchors in monotopic proteins using a SVM classifier, BMC Bioinformatics, 7:255.