Genome-Wide Functional Classification/Identification of Prokaryotic Transmembrane Proteins Based on Transmembrane Topology Similarity

Comprehensive Functional Classification/Identification of Prokaryotic Transmembrane Proteins by Sequence and Topology Similarities

About one fourth of genes in genomes has been known to encode transmembrane (TM) proteins (TMPs) [2, 6, 8]. Although TMPs have important functions playing an essential role in life, detailed and comprehensive analysis of their functions haven’t been carried out yet. In this study, we tried to develop a novel method to classify and identify TMP functions with use of TM topology similarity in add...

Comprehensive Functional Identification of Prokaryotic Transmembrane Proteins by Binary Topology Pattern

Comprehensive Functional Identification of Transmembrane Proteins Using the BTP Method

It has been revealed that TM protein functions correspond well to the TM topologies [the number of TM segments (tms), the loop length and the N-terminus location] [4, 5] and long loop regions contain functional domains. Recently, our group proposed a novel approach for classifying and identifying the functional classification and identification of TM protein functions based on TM topology infor...

A Consensus Transmembrane Topology Prediction Method of High-Reliability

It has been revealed that the function of transmembrane (TM) proteins (20-30% in most genomes [1]) can be classified and identified with the information of its TM topologies, i.e., the number of TM segments (TMSs), the position of TMS and the orientation of the TMS to the membrane lipid bilayer [6]. Therefore, developing the TM topology prediction method with high reliability is critical task f...

A combined transmembrane topology and signal peptide prediction method.

An inherent problem in transmembrane protein topology prediction and signal peptide prediction is the high similarity between the hydrophobic regions of a transmembrane helix and that of a signal peptide, leading to cross-reaction between the two types of predictions. To improve predictions further, it is therefore important to make a predictor that aims to discriminate between the two classes....