SiteFINDER

From DrugPedia: A Wikipedia for Drug discovery

siteFiNDER|3D is a web-based tool for predicting the location of functional sites in proteins.

CFG Analysis is a general method for predicting the location of functionally important sites within a target protein structure. Like other available structure/sequence analysis techniques, CFG Analysis exploits the evolutionary relationships present across groups of homologous proteins to identify regions that are likely to be of functional significance. However, this technique is particularly useful for situations where other methods fail, for instance when only a few or highly similar homologues can be identified. In such cases, a preliminary identification of functionally important sites may be coupled to a more detailed analysis of these regions with techniques that map evolutionarily conserved residues onto protein surfaces - such as Evolutionary Trace (ET) Analysis or ConSurf.

The siteFiNDER|3D Server requires, at a minimum, a query protein of known structure with coordinates in standard PDB format. In addition, a multiple sequence alignment in modified PIR format featuring homologues of the query protein may either be provided or generated automatically from sequences accumulated by the server.