What is different between INTREPID and other methods for predicting functional sites?
INTREPID belongs to the class of methods that predict functional residues using sequence information alone. Other methods that use only sequence information include Rate4Site (the core algorithm in the ConSurf webserver) and Evolutionary Trace. The basic idea underlying functional residue prediction based on evolutionary analysis is the observation that functionally important position tend to be more conserved across the protein family than the average position. INTREPID differs from other functional residue prediction methods in the way it uses the phylogenetic tree of the protein family. INTREPID’s tree traversal allows the identification of functional residues that are conserved within the family as well as those that are conserved within a subfamily but vary across subfamilies. Hence, INTREPID can be used to analyze highly divergent protein families. INTREPID does not rely on expert knowledge about which types of residues are likely to play specific functional roles, so it can be u
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