Functional annotation by identification of local surface similarities: a novel tool for structural genomics

Background: Protein function is often dependent on subsets of solvent-exposed residues that may exist in a similar three-dimensional configuration in non homologous proteins thus having different order and/or spacing in the sequence. Hence, functional annotation by means of sequence or fold similarity is not adequate for such cases. Results: We describe a method for the function-related annotation of protein structures by means of the detection of local structural similarity with a library of annotated functional sites. An automatic procedure was used to annotate the function of local surface regions. Next, we employed a sequence-independent algorithm to compare exhaustively these functional patches with a larger collection of protein surface cavities. After tuning and validating the algorithm on a dataset of well annotated structures, we applied it to a list of protein structures that are classified as being of unknown function in the Protein Data Bank. By this strategy, we were able...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Fabrizio Ferrè, Gabriele Ausiello, Andreas Zanzoni, Manuela Helmer-Citterich
• Keywords: BMCBI 2005, Protein, Protein Structures, Structural Similarity