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TranCEP: Predicting the substrate class of transmembrane transport proteins using compositional, evolutionary, and positional information

Title:

TranCEP: Predicting the substrate class of transmembrane transport proteins using compositional, evolutionary, and positional information

Alballa, Munira, Aplop, Faizah and Butler, Gregory (2020) TranCEP: Predicting the substrate class of transmembrane transport proteins using compositional, evolutionary, and positional information. PLOS ONE, 15 (1). e0227683. ISSN 1932-6203

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Official URL: http://dx.doi.org/10.1371/journal.pone.0227683

Abstract

Transporters mediate the movement of compounds across the membranes that separate the cell from its environment and across the inner membranes surrounding cellular compartments. It is estimated that one third of a proteome consists of membrane proteins, and many of these are transport proteins. Given the increase in the number of genomes being sequenced, there is a need for computational tools that predict the substrates that are transported by the transmembrane transport proteins. In this paper, we present TranCEP, a predictor of the type of substrate transported by a transmembrane transport protein. TranCEP combines the traditional use of the amino acid composition of the protein, with evolutionary information captured in a multiple sequence alignment (MSA), and restriction to important positions of the alignment that play a role in determining the specificity of the protein. Our experimental results show that TranCEP significantly outperforms the state-of-the-art predictors. The results quantify the contribution made by each type of information used.

Divisions:Concordia University > Gina Cody School of Engineering and Computer Science > Computer Science and Software Engineering
Item Type:Article
Refereed:Yes
Authors:Alballa, Munira and Aplop, Faizah and Butler, Gregory
Journal or Publication:PLOS ONE
Date:14 January 2020
Funders:
  • NSERC
  • Saudi Government
Digital Object Identifier (DOI):10.1371/journal.pone.0227683
ID Code:986462
Deposited By: GREGORY BUTLER
Deposited On:17 Mar 2020 15:24
Last Modified:17 Mar 2020 15:24
Related URLs:

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