FIEFDom: a transparent domain boundary recognition system using a fuzzy mean operator.

ABSTRACT: Protein domain prediction is often the preliminary step in both experimental and computational protein research. Here we present a new method to predict the domain boundaries of a multidomain protein from its amino acid sequence using a fuzzy mean operator. Using the nr-sequence database together with a reference protein set (RPS) containing known domain boundaries, the operator is used to assign a likelihood value for each residue of the query sequence as belonging to a domain boundary. This procedure robustly identifies contiguous boundary regions. For a dataset with a maximum sequence identity of 30%, the average domain prediction accuracy of our method is 97% for one domain proteins and 58% for multidomain proteins. The presented model is capable of using new sequence/structure informa

SUBMITTER: Bondugula R 

PROVIDER: S-EPMC2632928 | biostudies-literature | 2009 Feb

REPOSITORIES: biostudies-literature