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Rapid protein domain assignment from amino acid sequence using predicted secondary structure

Marsden, R. L., McGuffin, L. J. and Jones, D. T. (2009) Rapid protein domain assignment from amino acid sequence using predicted secondary structure. Protein Science, 11 (12). pp. 2814-2824. ISSN 09618368

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To link to this item DOI: 10.1110/ps.0209902


The elucidation of the domain content of a given protein sequence in the absence of determined structure or significant sequence homology to known domains is an important problem in structural biology. Here we address how successfully the delineation of continuous domains can be accomplished in the absence of sequence homology using simple baseline methods, an existing prediction algorithm (Domain Guess by Size), and a newly developed method (DomSSEA). The study was undertaken with a view to measuring the usefulness of these prediction methods in terms of their application to fully automatic domain assignment. Thus, the sensitivity of each domain assignment method was measured by calculating the number of correctly assigned top scoring predictions. We have implemented a new continuous domain identification method using the alignment of predicted secondary structures of target sequences against observed secondary structures of chains with known domain boundaries as assigned by Class Architecture Topology Homology (CATH). Taking top predictions only, the success rate of the method in correctly assigning domain number to the representative chain set is 73.3%. The top prediction for domain number and location of domain boundaries was correct for 24% of the multidomain set (±20 residues). These results have been put into context in relation to the results obtained from the other prediction methods assessed

Item Type:Article
Divisions:No Reading authors. Back catalogue items
ID Code:27438
Uncontrolled Keywords:Domains;secondary structure;protein folding;sequence analysis;structure prediction
Additional Information:The full text of this article is freely available via PMC using the link supplied in Related URLs

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