Predicting transmembrane helix packing arrangements using residue contacts and a force-directed algorithm.

ABSTRACT: Alpha-helical transmembrane proteins constitute roughly 30% of a typical genome and are involved in a wide variety of important biological processes including cell signalling, transport of membrane-impermeable molecules and cell recognition. Despite significant efforts to predict transmembrane protein topology, comparatively little attention has been directed toward developing a method to pack the helices together. Here, we present a novel approach to predict lipid exposure, residue contacts, helix-helix interactions and finally the optimal helical packing arrangement of transmembrane proteins. Using molecular dynamics data, we have trained and cross-validated a support vector machine (SVM) classifier to predict per residue lipid exposure with 69% accuracy. This information is combined wit

SUBMITTER: Nugent T 

PROVIDER: S-EPMC2841610 | biostudies-literature | 2010 Mar

REPOSITORIES: biostudies-literature