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    Results: 1 to 20 of 461

    1.

    Bioinformatic flowchart and database to investigate the origins and diversity of clan AA peptidases.

    Llorens C, Futami R, Renaud G, Moya A.

    Biol Direct. 2009 Jan 27;4:3.

    PMID:
    19173708
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    2.

    PASS2: an automated database of protein alignments organised as structural superfamilies.

    Bhaduri A, Pugalenthi G, Sowdhamini R.

    BMC Bioinformatics. 2004 Apr 2;5:35.

    PMID:
    15059245
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    3.

    The Gypsy Database (GyDB) of mobile genetic elements: release 2.0.

    Llorens C, Futami R, Covelli L, Domínguez-Escribá L, Viu JM, Tamarit D, Aguilar-Rodríguez J, Vicente-Ripolles M, Fuster G, Bernet GP, Maumus F, Munoz-Pomer A, Sempere JM, Latorre A, Moya A.

    Nucleic Acids Res. 2011 Jan;39(Database issue):D70-4. Epub 2010 Oct 29.

    PMID:
    21036865
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    4.

    The Gypsy Database (GyDB) of mobile genetic elements.

    Lloréns C, Futami R, Bezemer D, Moya A.

    Nucleic Acids Res. 2008 Jan;36(Database issue):D38-46. Epub 2007 Sep 25.

    PMID:
    17895280
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    5.

    MEROPS: the peptidase database.

    Rawlings ND, Tolle DP, Barrett AJ.

    Nucleic Acids Res. 2004 Jan 1;32(Database issue):D160-4.

    PMID:
    14681384
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    6.

    Relationships of gag-pol diversity between Ty3/Gypsy and Retroviridae LTR retroelements and the three kings hypothesis.

    Llorens C, Fares MA, Moya A.

    BMC Evol Biol. 2008 Oct 8;8:276.

    PMID:
    18842133
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    7.

    Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees.

    Llorens C, Muñoz-Pomer A, Bernad L, Botella H, Moya A.

    Biol Direct. 2009 Nov 2;4:41.

    PMID:
    19883502
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    8.

    MEROPS: the peptidase database.

    Rawlings ND, Barrett AJ.

    Nucleic Acids Res. 1999 Jan 1;27(1):325-31.

    PMID:
    9847218
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    9.

    Accurate domain identification with structure-anchored hidden Markov models, saHMMs.

    Tångrot JE, Kågström B, Sauer UH.

    Proteins. 2009 Aug 1;76(2):343-52.

    PMID:
    19173309
    [PubMed - indexed for MEDLINE]
    10.

    ProFAT: a web-based tool for the functional annotation of protein sequences.

    Bradshaw CR, Surendranath V, Habermann B.

    BMC Bioinformatics. 2006 Oct 23;7:466.

    PMID:
    17059594
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    11.

    Clan CD of cysteine peptidases as an example of evolutionary divergences in related protein families across plant clades.

    Cambra I, Garcia FJ, Martinez M.

    Gene. 2010 Jan 1;449(1-2):59-69. Epub 2009 Sep 12.

    PMID:
    19751811
    [PubMed - indexed for MEDLINE]
    12.

    Evolution of a "conserved" amino acid sequence: a model study of an in silico investigation of the phylogenesis of some immune receptors.

    Panaro MA, Acquafredda A, Sisto M, Lisi S, Saccia M, Mitolo V.

    Curr Pharm Des. 2006;12(32):4091-121.

    PMID:
    17100614
    [PubMed - indexed for MEDLINE]
    13.

    Bioinformatic analysis of the neprilysin (M13) family of peptidases reveals complex evolutionary and functional relationships.

    Bland ND, Pinney JW, Thomas JE, Turner AJ, Isaac RE.

    BMC Evol Biol. 2008 Jan 23;8:16.

    PMID:
    18215274
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    14.

    The Bet v 1 fold: an ancient, versatile scaffold for binding of large, hydrophobic ligands.

    Radauer C, Lackner P, Breiteneder H.

    BMC Evol Biol. 2008 Oct 15;8:286.

    PMID:
    18922149
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    15.

    Novel predicted peptidases with a potential role in the ubiquitin signaling pathway.

    Iyer LM, Koonin EV, Aravind L.

    Cell Cycle. 2004 Nov;3(11):1440-50. Epub 2004 Nov 6.

    PMID:
    15483401
    [PubMed - indexed for MEDLINE]
    Free Article
    16.

    The MEROPS database as a protease information system.

    Barrett AJ, Rawlings ND, O'Brien EA.

    J Struct Biol. 2001 May-Jun;134(2-3):95-102. Review.

    PMID:
    11551172
    [PubMed - indexed for MEDLINE]
    17.

    Clustering the annotation space of proteins.

    Kunin V, Ouzounis CA.

    BMC Bioinformatics. 2005 Feb 9;6:24.

    PMID:
    15703069
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    18.

    Type II restriction endonuclease R.Hpy188I belongs to the GIY-YIG nuclease superfamily, but exhibits an unusual active site.

    Kaminska KH, Kawai M, Boniecki M, Kobayashi I, Bujnicki JM.

    BMC Struct Biol. 2008 Nov 14;8:48.

    PMID:
    19014591
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    19.

    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
    20.

    HMMerThread: detecting remote, functional conserved domains in entire genomes by combining relaxed sequence-database searches with fold recognition.

    Bradshaw CR, Surendranath V, Henschel R, Mueller MS, Habermann BH.

    PLoS One. 2011 Mar 10;6(3):e17568.

    PMID:
    21423752
    [PubMed - indexed for MEDLINE]
    Free PMC Article

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