Prediction of the burial status of transmembrane residues of helical membrane proteins.

ABSTRACT:

Background

Helical membrane proteins (HMPs) play a crucial role in diverse cellular processes, yet it still remains extremely difficult to determine their structures by experimental techniques. Given this situation, it is highly desirable to develop sequence-based computational methods for predicting structural characteristics of HMPs.

Results

We have developed TMX (TransMembrane eXposure), a novel method for predicting the burial status (i.e. buried in the protein structure vs. exposed to the membrane) of transmembrane (TM) residues of HMPs. TMX derives positional scores of TM residues based on their profiles and conservation indices. Then, a support vector classifier is used for predicting their burial status. Its prediction accuracy is 78.71% on a benchmark data set, repr

SUBMITTER: Park Y 

PROVIDER: S-EPMC2000914 | biostudies-literature | 2007 Aug

REPOSITORIES: biostudies-literature