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  • The proteome: structure, function and evolution
  • Fleming K; Kelley LA; Islam SA; MacCallum RM; Muller A; Pazos F; Sternberg MJ
  • Philos Trans R Soc Lond B Biol Sci 2006[Mar]; 361 (1467): 441-51
  • This 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]





  • *{{pmid16524832}}
    *<b>[http://www.kidney.de/mlpefetch.php?search=16524832 The proteome: structure, function and evolution ]</b> Philos Trans R Soc Lond B Biol Sci 2006; 361(1467) ; 441-51 Fleming K; Kelley LA; Islam SA; MacCallum RM; Muller A; Pazos F; Sternberg MJ

        *16524832*

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    Philos Trans R Soc Lond B Biol Sci

    441 1467.361 2006