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lüll The proteome: structure, function and evolution Fleming K; Kelley LA; Islam SA; MacCallum RM; Muller A; Pazos F; Sternberg MJPhilos Trans R Soc Lond B Biol Sci 2006[Mar]; 361 (1467): 441-51This paper reports two studies to model the inter-relationships between protein sequence, structure and function. First, an automated pipeline to provide a structural annotation of proteomes in the major genomes is described. The results are stored in a database at Imperial College, London (3D-GENOMICS) that can be accessed at www.sbg.bio.ic.ac.uk. Analysis of the assignments to structural superfamilies provides evolutionary insights. 3D-GENOMICS is being integrated with related proteome annotation data at University College London and the European Bioinformatics Institute in a project known as e-protein (http://www.e-protein.org/). The second topic is motivated by the developments in structural genomics projects in which the structure of a protein is determined prior to knowledge of its function. We have developed a new approach PHUNCTIONER that uses the gene ontology (GO) classification to supervise the extraction of the sequence signal responsible for protein function from a structure-based sequence alignment. Using GO we can obtain profiles for a range of specificities described in the ontology. In the region of low sequence similarity (around 15%), our method is more accurate than assignment from the closest structural homologue. The method is also able to identify the specific residues associated with the function of the protein family.|*Evolution, Molecular[MESH]|Computational Biology[MESH]|Multigene Family[MESH]|Protein Structure, Tertiary[MESH]|Proteome/*chemistry/genetics/*metabolism[MESH]|Sequence Homology[MESH] |