Predicting functional sites with an automated algorithm suitable for heterogeneous datasets

Background: In a previous report (La et al., Proteins, 2005), we have demonstrated that the identification of phylogenetic motifs, protein sequence fragments conserving the overall familial phylogeny, represent a promising approach for sequence/function annotation. Across a structurally and functionally heterogeneous dataset, phylogenetic motifs have been demonstrated to correspond to a wide variety of functional site archetypes, including those defined by surface loops, active site clefts, and less exposed regions. However, in our original demonstration of the technique, phylogenetic motif identification is dependent upon a manually determined similarity threshold, prohibiting large-scale application of the technique. Results: In this report, we present an algorithmic approach that determines thresholds without human subjectivity. The approach relies on significant raw data preprocessing to improve signal detection. Subsequently, Partition Around Medoids Clustering (PAMC) of the simi...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: David La, Dennis R. Livesay
• Keywords: BMCBI 2005, Functional Site, Phylogenetic Motif, Phylogenetic Motif Identification