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    Results: 1 to 20 of 109

    2.

    Strategies for the effective identification of remotely related sequences in multiple PSSM search approach.

    Gowri VS, Tina KG, Krishnadev O, Srinivasan N.

    Proteins. 2007 Jun 1;67(4):789-94.

    PMID:
    17380509
    [PubMed - indexed for MEDLINE]
    3.

    MulPSSM: a database of multiple position-specific scoring matrices of protein domain families.

    Gowri VS, Krishnadev O, Swamy CS, Srinivasan N.

    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D243-6.

    PMID:
    16381855
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    4.

    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
    5.

    SUPFAM: a database of sequence superfamilies of protein domains.

    Pandit SB, Bhadra R, Gowri VS, Balaji S, Anand B, Srinivasan N.

    BMC Bioinformatics. 2004 Mar 15;5:28.

    PMID:
    15113407
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    6.

    SUPFAM--a database of potential protein superfamily relationships derived by comparing sequence-based and structure-based families: implications for structural genomics and function annotation in genomes.

    Pandit SB, Gosar D, Abhiman S, Sujatha S, Dixit SS, Mhatre NS, Sowdhamini R, Srinivasan N.

    Nucleic Acids Res. 2002 Jan 1;30(1):289-93.

    PMID:
    11752317
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    7.

    Pfam: a comprehensive database of protein domain families based on seed alignments.

    Sonnhammer EL, Eddy SR, Durbin R.

    Proteins. 1997 Jul;28(3):405-20.

    PMID:
    9223186
    [PubMed - indexed for MEDLINE]
    8.

    PHOG-BLAST--a new generation tool for fast similarity search of protein families.

    Merkeev IV, Mironov AA.

    BMC Evol Biol. 2006 Jun 22;6:51.

    PMID:
    16792802
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    9.

    Use of multiple profiles corresponding to a sequence alignment enables effective detection of remote homologues.

    Anand B, Gowri VS, Srinivasan N.

    Bioinformatics. 2005 Jun 15;21(12):2821-6. Epub 2005 Apr 7.

    PMID:
    15817691
    [PubMed - indexed for MEDLINE]
    Free Article
    10.

    PSSM-based prediction of DNA binding sites in proteins.

    Ahmad S, Sarai A.

    BMC Bioinformatics. 2005 Feb 19;6:33.

    PMID:
    15720719
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    11.

    Fast model-based protein homology detection without alignment.

    Hochreiter S, Heusel M, Obermayer K.

    Bioinformatics. 2007 Jul 15;23(14):1728-36. Epub 2007 May 8.

    PMID:
    17488755
    [PubMed - indexed for MEDLINE]
    Free Article
    12.

    Significant speedup of database searches with HMMs by search space reduction with PSSM family models.

    Beckstette M, Homann R, Giegerich R, Kurtz S.

    Bioinformatics. 2009 Dec 15;25(24):3251-8. Epub 2009 Oct 14.

    PMID:
    19828575
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    13.

    IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices.

    Schäffer AA, Wolf YI, Ponting CP, Koonin EV, Aravind L, Altschul SF.

    Bioinformatics. 1999 Dec;15(12):1000-11.

    PMID:
    10745990
    [PubMed - indexed for MEDLINE]
    Free Article
    14.

    Embedding strategies for effective use of information from multiple sequence alignments.

    Henikoff S, Henikoff JG.

    Protein Sci. 1997 Mar;6(3):698-705.

    PMID:
    9070452
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    15.

    Fast index based algorithms and software for matching position specific scoring matrices.

    Beckstette M, Homann R, Giegerich R, Kurtz S.

    BMC Bioinformatics. 2006 Aug 24;7:389.

    PMID:
    16930469
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    16.

    A structure-based method for protein sequence alignment.

    Kann MG, Thiessen PA, Panchenko AR, Schäffer AA, Altschul SF, Bryant SH.

    Bioinformatics. 2005 Apr 15;21(8):1451-6. Epub 2004 Dec 21.

    PMID:
    15613392
    [PubMed - indexed for MEDLINE]
    Free Article
    17.

    A comparison of position-specific score matrices based on sequence and structure alignments.

    Panchenko AR, Bryant SH.

    Protein Sci. 2002 Feb;11(2):361-70.

    PMID:
    11790846
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    18.

    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]
    19.

    CDD: a curated Entrez database of conserved domain alignments.

    Marchler-Bauer A, Anderson JB, DeWeese-Scott C, Fedorova ND, Geer LY, He S, Hurwitz DI, Jackson JD, Jacobs AR, Lanczycki CJ, Liebert CA, Liu C, Madej T, Marchler GH, Mazumder R, Nikolskaya AN, Panchenko AR, Rao BS, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Vasudevan S, Wang Y, Yamashita RA, Yin JJ, Bryant SH.

    Nucleic Acids Res. 2003 Jan 1;31(1):383-7.

    PMID:
    12520028
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    20.

    PASS2: a semi-automated database of protein alignments organised as structural superfamilies.

    Mallika V, Bhaduri A, Sowdhamini R.

    Nucleic Acids Res. 2002 Jan 1;30(1):284-8.

    PMID:
    11752316
    [PubMed - indexed for MEDLINE]
    Free PMC Article

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