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      Protein function annotation by homology-based inference

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          Abstract

          Where information on homologous proteins is available, progress is being made in automated prediction of protein function from sequence and structure.

          Abstract

          With many genomes now sequenced, computational annotation methods to characterize genes and proteins from their sequence are increasingly important. The BioSapiens Network has developed tools to address all stages of this process, and here we review progress in the automated prediction of protein function based on protein sequence and structure.

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          Most cited references61

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          Gene Ontology: tool for the unification of biology

          Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.
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            CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues

            Cavities on a proteins surface as well as specific amino acid positioning within it create the physicochemical properties needed for a protein to perform its function. CASTp () is an online tool that locates and measures pockets and voids on 3D protein structures. This new version of CASTp includes annotated functional information of specific residues on the protein structure. The annotations are derived from the Protein Data Bank (PDB), Swiss-Prot, as well as Online Mendelian Inheritance in Man (OMIM), the latter contains information on the variant single nucleotide polymorphisms (SNPs) that are known to cause disease. These annotated residues are mapped to surface pockets, interior voids or other regions of the PDB structures. We use a semi-global pair-wise sequence alignment method to obtain sequence mapping between entries in Swiss-Prot, OMIM and entries in PDB. The updated CASTp web server can be used to study surface features, functional regions and specific roles of key residues of proteins.
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              Protein structure alignment by incremental combinatorial extension (CE) of the optimal path.

              A new algorithm is reported which builds an alignment between two protein structures. The algorithm involves a combinatorial extension (CE) of an alignment path defined by aligned fragment pairs (AFPs) rather than the more conventional techniques using dynamic programming and Monte Carlo optimization. AFPs, as the name suggests, are pairs of fragments, one from each protein, which confer structure similarity. AFPs are based on local geometry, rather than global features such as orientation of secondary structures and overall topology. Combinations of AFPs that represent possible continuous alignment paths are selectively extended or discarded thereby leading to a single optimal alignment. The algorithm is fast and accurate in finding an optimal structure alignment and hence suitable for database scanning and detailed analysis of large protein families. The method has been tested and compared with results from Dali and VAST using a representative sample of similar structures. Several new structural similarities not detected by these other methods are reported. Specific one-on-one alignments and searches against all structures as found in the Protein Data Bank (PDB) can be performed via the Web at http://cl.sdsc.edu/ce.html.
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                Author and article information

                Journal
                Genome Biol
                Genome Biology
                BioMed Central
                1465-6906
                1465-6914
                2009
                2 February 2009
                : 10
                : 2
                : 207
                Affiliations
                [1 ]Department of Biological Chemistry, The Hebrew University of Jerusalem, Sudarsky Center, Jerusalem 91904, Israel
                [2 ]Department of Biochemical Sciences, University of Rome "La Sapienza", Rome 00185, Italy
                [3 ]Research Department of Structural and Molecular Biology, University College, London WC1E, UK
                [4 ]European Bioinformatics Institute, Hinxton CB10 1SD, UK
                [5 ]Technische Universität, Munich, Germany
                [6 ]Helmholtz Zentrum, German Research Center for Environmental Health, Munich 85764, Germany
                [7 ]Pasteur Institute-Cenci Bolognetti Foundation, University of Rome "La Sapienza", Rome 00185, Italy
                Article
                gb-2009-10-2-207
                10.1186/gb-2009-10-2-207
                2688287
                19226439
                5b0db009-807c-4ceb-909d-30922ce22192
                Copyright © 2009 BioMed Central Ltd
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                Review

                Genetics
                Genetics

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