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Domain parsing, or the detection of signals of protein structural domains from sequence data, is a complex and difficult problem. If carried out reliably it would be a powerful interpretive and predictive tool for genomic and proteomic studies. We report on a novel approach to domain parsing using consensus techniques based on Hidden Markov Models (HMMs) and BLAST searches built from a training set of 1471 continuous structural domains from the Dali Domain Dictionary (DDD). Validation on an independent test sample of family-matched structural domain sequences from the Scop database yields a consensus prediction performance rate of 75.5%, well above the 58% obtained by simple agreement of methods.

Protein Structural Domain Parsing by Consensus Reasoning over Multiple Knowledge Sources and Methods