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    Results: 1 to 20 of 172

    1.

    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]Related articlesFree article

    2.

    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]Related articlesFree article

    3.

    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]Related articlesFree article

    4.

    Automatic annotation of protein function based on family identification.

    Abascal F, Valencia A.

    Proteins. 2003 Nov 15;53(3):683-92.PMID: 14579359 [PubMed - indexed for MEDLINE]Related articles

    5.

    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]Related articlesFree article

    6.

    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]Related articlesFree article

    7.

    MACHOS: Markov clusters of homologous subsequences.

    Wong S, Ragan MA.

    Bioinformatics. 2008 Jul 1;24(13):i77-85.PMID: 18586748 [PubMed - indexed for MEDLINE]Related articlesFree article

    8.

    Hidden Markov models for detecting remote protein homologies.

    Karplus K, Barrett C, Hughey R.

    Bioinformatics. 1998;14(10):846-56.PMID: 9927713 [PubMed - indexed for MEDLINE]Related articlesFree article

    9.

    CLUSS: clustering of protein sequences based on a new similarity measure.

    Kelil A, Wang S, Brzezinski R, Fleury A.

    BMC Bioinformatics. 2007 Aug 4;8:286.PMID: 17683581 [PubMed - indexed for MEDLINE]Related articlesFree article

    10.

    Clustering protein sequences--structure prediction by transitive homology.

    Bolten E, Schliep A, Schneckener S, Schomburg D, Schrader R.

    Bioinformatics. 2001 Oct;17(10):935-41.PMID: 11673238 [PubMed - indexed for MEDLINE]Related articlesFree article

    11.

    SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition.

    Melvin I, Ie E, Kuang R, Weston J, Stafford WN, Leslie C.

    BMC Bioinformatics. 2007 May 22;8 Suppl 4:S2.PMID: 17570145 [PubMed - indexed for MEDLINE]Related articlesFree article

    12.

    Phylogenomic inference of protein molecular function.

    Krishnamurthy N, Sjölander K.

    Curr Protoc Bioinformatics. 2005 Oct;Chapter 6:Unit 6.9.PMID: 18428751 [PubMed - indexed for MEDLINE]Related articles

    13.

    Protein domain identification and improved sequence similarity searching using PSI-BLAST.

    George RA, Heringa J.

    Proteins. 2002 Sep 1;48(4):672-81.PMID: 12211035 [PubMed - indexed for MEDLINE]Related articles

    14.

    STRALCP--structure alignment-based clustering of proteins.

    Zemla A, Geisbrecht B, Smith J, Lam M, Kirkpatrick B, Wagner M, Slezak T, Zhou CE.

    Nucleic Acids Res. 2007;35(22):e150. Epub 2007 Nov 26.PMID: 18039711 [PubMed - indexed for MEDLINE]Related articlesFree article

    15.

    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]Related articlesFree article

    16.

    Super paramagnetic clustering of protein sequences.

    Tetko IV, Facius A, Ruepp A, Mewes HW.

    BMC Bioinformatics. 2005 Apr 1;6:82.PMID: 15804359 [PubMed - indexed for MEDLINE]Related articlesFree article

    17.

    DOMAC: an accurate, hybrid protein domain prediction server.

    Cheng J.

    Nucleic Acids Res. 2007 Jul;35(Web Server issue):W354-6. Epub 2007 Jun 6.PMID: 17553833 [PubMed - indexed for MEDLINE]Related articlesFree article

    18.

    FastBLAST: homology relationships for millions of proteins.

    Price MN, Dehal PS, Arkin AP.

    PLoS One. 2008;3(10):e3589. Epub 2008 Oct 31.PMID: 18974889 [PubMed - indexed for MEDLINE]Related articlesFree article

    19.

    eBLOCKs: enumerating conserved protein blocks to achieve maximal sensitivity and specificity.

    Su QJ, Lu L, Saxonov S, Brutlag DL.

    Nucleic Acids Res. 2005 Jan 1;33(Database issue):D178-82.PMID: 15608172 [PubMed - indexed for MEDLINE]Related articlesFree article

    20.

    FunShift: a database of function shift analysis on protein subfamilies.

    Abhiman S, Sonnhammer EL.

    Nucleic Acids Res. 2005 Jan 1;33(Database issue):D197-200.PMID: 15608176 [PubMed - indexed for MEDLINE]Related articlesFree article

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