Abstract
Alpha-helical transmembrane proteins mediate many key biological processes and represent 20%–30% of all genes in many organisms. Due to the difficulties in experimentally determining their high-resolution 3D structure, computational methods to predict the location and orientation of transmembrane helix segments using sequence information are essential. We present, TOPTMH a new transmembrane helix topology prediction method that combines support vector machines, hidden Markov models, and a widely-used rule-based scheme. The contribution of this work is the development of a prediction approach that first uses a binary SVM classifier to predict the helix residues and then it employs a pair of HMM models that incorporate the SVM predictions and hydropathy-based features to identify the entire transmembrane helix segments by capturing the structural characteristics of these proteins. TOPTMH outperforms state-of-the-art prediction methods and achieves the best performance on an independent static benchmark.
This work was supported by NSF EIA-9986042, ACI-0133464, IIS-0431135, NIH RLM008713A, NIH T32GM008347, the Digital Technology Center, University of Minnesota and the Minnesota Supercomputing Institute.
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Keywords
- Hide Markov Model
- Hide Markov Model Model
- Helical Segment
- Membrane Protein Structure
- Topology Prediction
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
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Ahmed, R., Rangwala, H., Karypis, G. (2008). TOPTMH: Topology Predictor for Transmembrane α-Helices. In: Daelemans, W., Goethals, B., Morik, K. (eds) Machine Learning and Knowledge Discovery in Databases. ECML PKDD 2008. Lecture Notes in Computer Science(), vol 5211. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-87479-9_20
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