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    Results: 1 to 20 of 125

    1.

    PhyloFacts: an online structural phylogenomic encyclopedia for protein functional and structural classification.

    Krishnamurthy N, Brown DP, Kirshner D, Sjölander K.

    Genome Biol. 2006;7(9):R83.

    PMID:
    16973001
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    2.

    Automated protein subfamily identification and classification.

    Brown DP, Krishnamurthy N, Sjölander K.

    PLoS Comput Biol. 2007 Aug;3(8):e160.

    PMID:
    17708678
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    3.

    Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis.

    Glanville JG, Kirshner D, Krishnamurthy N, Sjölander K.

    Nucleic Acids Res. 2007 Jul;35(Web Server issue):W27-32. Epub 2007 May 8.

    PMID:
    17488835
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    4.

    Phylogenomic inference of protein molecular function: advances and challenges.

    Sjölander K.

    Bioinformatics. 2004 Jan 22;20(2):170-9. Review.

    PMID:
    14734307
    [PubMed - indexed for MEDLINE]
    Free Article
    5.

    FlowerPower: clustering proteins into domain architecture classes for phylogenomic inference of protein function.

    Krishnamurthy N, Brown D, Sjölander K.

    BMC Evol Biol. 2007 Feb 8;7 Suppl 1:S12.

    PMID:
    17288570
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    6.

    Phylomat: an automated protein motif analysis tool for phylogenomics.

    Graham WV, Tcheng DK, Shirk AL, Attene-Ramos MS, Welge ME, Gaskins HR.

    J Proteome Res. 2004 Nov-Dec;3(6):1289-91.

    PMID:
    15595740
    [PubMed - indexed for MEDLINE]
    7.

    ELISA: structure-function inferences based on statistically significant and evolutionarily inspired observations.

    Shakhnovich BE, Harvey JM, Comeau S, Lorenz D, DeLisi C, Shakhnovich E.

    BMC Bioinformatics. 2003 Sep 2;4:34. Epub 2003 Sep 2.

    PMID:
    12952559
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    8.

    PIRSF: family classification system at the Protein Information Resource.

    Wu CH, Nikolskaya A, Huang H, Yeh LS, Natale DA, Vinayaka CR, Hu ZZ, Mazumder R, Kumar S, Kourtesis P, Ledley RS, Suzek BE, Arminski L, Chen Y, Zhang J, Cardenas JL, Chung S, Castro-Alvear J, Dinkov G, Barker WC.

    Nucleic Acids Res. 2004 Jan 1;32(Database issue):D112-4.

    PMID:
    14681371
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    9.

    INTREPID--INformation-theoretic TREe traversal for Protein functional site IDentification.

    Sankararaman S, Sjölander K.

    Bioinformatics. 2008 Nov 1;24(21):2445-52. Epub 2008 Sep 6.

    PMID:
    18776193
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    10.

    Gene3D: modelling protein structure, function and evolution.

    Yeats C, Maibaum M, Marsden R, Dibley M, Lee D, Addou S, Orengo CA.

    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D281-4.

    PMID:
    16381865
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    11.

    SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny.

    Wilson D, Pethica R, Zhou Y, Talbot C, Vogel C, Madera M, Chothia C, Gough J.

    Nucleic Acids Res. 2009 Jan;37(Database issue):D380-6. Epub 2008 Nov 26.

    PMID:
    19036790
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    12.

    The apoptosis database.

    Doctor KS, Reed JC, Godzik A, Bourne PE.

    Cell Death Differ. 2003 Jun;10(6):621-33. Review.

    PMID:
    12761571
    [PubMed - indexed for MEDLINE]
    Free Article
    13.

    The evolution of protein functions and networks: a family-centric approach.

    Dessailly BH, Reid AJ, Yeats C, Lees JG, Cuff A, Orengo CA.

    Biochem Soc Trans. 2009 Aug;37(Pt 4):745-50.

    PMID:
    19614587
    [PubMed - indexed for MEDLINE]
    14.

    Protein families and their evolution-a structural perspective.

    Orengo CA, Thornton JM.

    Annu Rev Biochem. 2005;74:867-900. Review.

    PMID:
    15954844
    [PubMed - indexed for MEDLINE]
    15.

    ELISA: a unified, multidimensional view of the protein domain universe.

    Shakhnovich BE, Harvey JM, Delisi C.

    Genome Inform. 2004;15(1):213-20.

    PMID:
    15712123
    [PubMed - indexed for MEDLINE]
    16.

    fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies.

    Tung CH, Yang JM.

    Nucleic Acids Res. 2007 Jul;35(Web Server issue):W438-43. Epub 2007 May 7.

    PMID:
    17485476
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    17.

    Subfamily hmms in functional genomics.

    Brown D, Krishnamurthy N, Dale JM, Christopher W, Sjölander K.

    Pac Symp Biocomput. 2005:322-33.

    PMID:
    15759638
    [PubMed - indexed for MEDLINE]
    Free Article
    18.

    Allergens are distributed into few protein families and possess a restricted number of biochemical functions.

    Radauer C, Bublin M, Wagner S, Mari A, Breiteneder H.

    J Allergy Clin Immunol. 2008 Apr;121(4):847-52.e7.

    PMID:
    18395549
    [PubMed - indexed for MEDLINE]
    19.

    Data growth and its impact on the SCOP database: new developments.

    Andreeva A, Howorth D, Chandonia JM, Brenner SE, Hubbard TJ, Chothia C, Murzin AG.

    Nucleic Acids Res. 2008 Jan;36(Database issue):D419-25. Epub 2007 Nov 13.

    PMID:
    18000004
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    20.

    The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures.

    Goldenberg O, Erez E, Nimrod G, Ben-Tal N.

    Nucleic Acids Res. 2009 Jan;37(Database issue):D323-7. Epub 2008 Oct 29.

    PMID:
    18971256
    [PubMed - indexed for MEDLINE]
    Free PMC Article

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