Bioinformatics Research and Development pp 292-302
Prediction of Structurally-Determined Coiled-Coil Domains with Hidden Markov Models
The coiled-coil protein domain is a widespread structural motif known to be involved in a wealth of key interactions in cells and organisms. Coiled-coil recognition and prediction of their location in a protein sequence are important steps for modeling protein structure and function. Nowadays, thanks to the increasing number of experimentally determined protein structures, a significant number of coiled-coil protein domains is available. This enables the development of methods suited to predict the coiled-coil structural motifs starting from the protein sequence. Several methods have been developed to predict classical heptads using manually annotated coiled-coil domains. In this paper we focus on the prediction structurally-determined coiled-coil segments. We introduce a new method based on hidden Markov models that complement the existing methods and outperforms them in the task of locating structurally-defined coiled-coil segments.
KeywordsProtein structure prediction Hidden Markov models coiled-coil domains
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- 1.Lupas, A.: Coiled coils: new structures and new functions. Trends Biochem Sci. 21, 375–382 (1996)Google Scholar
- 8.Delorenzi, M., Speed, T.: An HMM model for coiled-coil domains and a comparison with PSSM-based predictions. Bioinformatics, 617–625 (2002)Google Scholar
- 12.Lupas, A.N., Gruber, M.: The structure of alpha-helical coiled coils. Adv. Protein Chem. 70, 37–78 (2005)Google Scholar
- 13.Durbin, R., Eddy, S., Krogh, A., Mitchinson, G.: Biological sequence analysis: probabilistic models of proteins and nucleic acids. Cambridge Univ. Press, CambridgeGoogle Scholar