ConPred_elite: a highly reliable approach to transmembrane topology predication.
The function of transmembrane (TM) proteins is closely correlated to their TM topology; large quantities of highly reliable TM topology data are becoming increasingly required. We present a new consensus approach for TM topology prediction (ConPred_elite) that can predict the whole topology with accuracies of 0.98 for prokaryotic and 0.95 for eukaryotic proteins on a dataset of experimentally-characterized TM topologies. The predicted yield on the dataset is 30.4% for prokaryotic and 21.5% for eukaryotic proteins. Applying ConPred_elite to predicted TM proteins extracted from 29 prokaryotic and 10 eukaryotic proteomes, we obtained 3871 and 7271 highly reliable TM topologies (yields, 19.8 and 13.3%), respectively. The predicted TM topology data may contribute to further research into a comprehensive functional classification and identification of TM proteins based on information of the topology.
Xia
Jun-Xiong
JX
Department of Electronic and Information System Engineering, Faculty of Science and Technology, Hirosaki University, Hirosaki 036-8561,Japan.
Ikeda
Masami
M
Shimizu
Toshio
T
D019843:Archaeal Proteins / Q000235:genetics; D001426:Bacterial Proteins / Q000235:genetics; D002462:Cell Membrane / Q000737:chemistry*; D016384:Consensus Sequence; D016208:Databases, Factual; D005057:Eukaryotic Cells; D016678:Genome; D008565:Membrane Proteins / Q000737:chemistry* / Q000145:classification / Q000235:genetics; D011237:Predictive Value of Tests; D011387:Prokaryotic Cells; D020543:Proteome / Q000235:genetics
D019843:Archaeal Proteins; D001426:Bacterial Proteins; D008565:Membrane Proteins; D020543:Proteome