Remote homology detection

Key words Helicobacter pylori, Proteins, Remote homology detection, Function assignment... 

In some proteins, only a part of the H. pylori protein is assigned a functional domain by Pfam and the rest of the protein is not assigned any function. Remote homology detection methods employed in the current analysis have established relationships between these unassigned regions and Pfam domain families. 

The following sections briefly discuss some results and trends in using structure prediction for remote homology detection especially in the genomic context, to aid the structural genomics projects, to further whole genome annotation and to exploit the sequence-to-structure-to-function paradigm for functional predictions. 

Madera, M., and J. Gough. 2002. A comparison of profile hidden Markov model procedures for remote homology detection. Nucleic Acids Res 30 4312-28. 

Kuang, R., le, E., Wang, K., Wang, K., Siddiqi, M., Freund, Y., Leslie, C. Profile-based string kernels for remote homology detection and motif extraction. J. Bioinform. Gomput. Biol. 2005, 3,527-50. 

Rangwala, H., Karypis, G. Profile-based direct kernels for remote homology detection and fold recognition. Bioinformatics 2005, 21, 4239 7. 

Hou, Y, Hsu, W, Lee, M.L., Bystroff, C. Efficient remote homology detection using local structure. Bioinformatics 2003,19,2294-301. 

Ben-Hur, A., Brutlag, D. Remote homology detection A motif based approach, in International Conference on Intelligent Systems for Molecular Biology, vol. 11,2003, pp. suppl l 126-33. 

Wistrand M et al (2006) A general model of G protein-coupled receptor sequences and its application to detect remote homologs. Protein Sci 15 509-521 Wong ST et al (2000) Disruption of the type III adenylyl cyclase gene leads to peripheral and behavioral anosmia in transgenic mice. Neuron 27 487-497 Xu P et al (2005) Drosophila OBP LUSH is required for activity of pheromone-sensitive neurons. Neuron 45 193-200... 

Soeding, J., and A. N. Lupas. 2004. Homology search by HMM-HMM comparison detects more than three times as many remote homologs as PSIBLAST or HMMER. Abstract No. 41. 3DSIG Structural Bioinformatics Meeting at ISMB. 

If no remote homolog can be detected for U, we are forced to simplify the prediction problem. There is a pay-off from making this simplification using the rich diversity of information in current databases, it is possible to make very accurate ID predictions from the sequence alone. Automatic prediction services are readily available for secondary structure, solvent accessibility, location and topology for transmembrane helices, and the location of helices for the special class of coiled-coil proteins, ... 

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