Introduction

Transmembrane proteins such as transporters and channels mediate the passage of inorganic and organic substances across biological membranes through their central pore. Pore-lining residues (PLRs) that make direct contacts to the substrates have a crucial impact on the function of the protein and, hence, their identification is a key step in mechanistic studies. Here, we established a nonredundant data set containing the three-dimensional (3D) structures of 90 α-helical transmembrane proteins and annotated the PLRs of these proteins by a pore identification software. A support vector machine was then trained to distinguish PLRs from other residues based on the protein sequence alone. Using sixfold cross-validation, our best performing predictor gave a Matthews's correlation coefficient of 0.41 with an accuracy of 0.86, sensitivity of 0.61, and specificity of 0.89, respectively. We provide a novel software tool that will aid biomedical scientists working on transmembrane proteins with unknown 3D structures. Both standalone version and web service are freely available from the URL http://service.bioinformatik.uni-saarland.de/PRIMSIPLR/.

Publications

  1. PRIMSIPLR: prediction of inner-membrane situated pore-lining residues for alpha-helical transmembrane proteins.
    Cite this
    Nguyen D, Helms V, Lee PH, 2014-07-01 - Proteins

Credits

  1. Duy Nguyen
    Developer

    Center for Bioinformatics, Saarland University, Germany

  2. Volkhard Helms
    Developer

  3. Po-Hsien Lee
    Investigator

Community Ratings

UsabilityEfficiencyReliabilityRated By
0 user
Sign in to rate
Summary
AccessionBT006340
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesPerl
User InterfaceTerminal Command Line
Download Count0
Submitted ByPo-Hsien Lee