Abstract
BackgroundTransmembrane (TM) proteins are proteins that span a biological membrane one or more times. As their 3-D structures are hard to determine, experiments focus on identifying their topology (i. e. which parts of the amino acid sequence are buried in the membrane and which are located on either side of the membrane), but only a few topologies are known. Consequently, various computational TM topology predictors have been developed, but their accuracies are far from perfect. The prediction quality can be improved by applying a consensus approach, which combines results of several predictors to yield a more reliable result.ResultsA novel TM consensus method, named MetaTM, is proposed in this work. MetaTM is based on support vector machine models and combines the results of six TM topology predictors and two signal peptide predictors. On a large data set comprising 1460 sequences of TM proteins with known topologies and 2362 globular protein sequences it correctly predicts 86.7% of all topologies.ConclusionCombining several TM predictors in a consensus prediction framework improves overall accuracy compared to any of the individual methods. Our proposed SVM-based system also has higher accuracy than a previous consensus predictor. MetaTM is made available both as downloadable source code and as DAS server at
Highlights
Transmembrane (TM) proteins are proteins that span a biological membrane one or more times
The MetaTM algorithm On the top level the consensus prediction is split into two major parts: (1) the segments consensus for finding TM segments and signal peptides (SPs), and (2) the N-terminal consensus
We have presented a novel TM consensus method, MetaTM, that predicts the transmembrane topology and signal peptides based on the results of seven single predictors
Summary
Transmembrane (TM) proteins are proteins that span a biological membrane one or more times As their 3-D structures are hard to determine, experiments focus on identifying their topology Transmembrane proteins are proteins that span the biological membrane one or more times. All communication and transportation between the inside and the outside of a cell is mediated by them They are vital for cell recognition and cell adhesion and serve as receptors. This makes them especially interesting for medicine, since almost half of all present-day drug targets are TM proteins [3]. TM proteins make up about a fifth of all known protein (page number not for citation purposes)
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