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    Results: 1 to 20 of 378

    1.

    Subfamily specific conservation profiles for proteins based on n-gram patterns.

    Vries JK, Liu X.

    BMC Bioinformatics. 2008 Jan 30;9:72.PMID: 18234090 [PubMed - indexed for MEDLINE]Related articlesFree 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]Related articlesFree article

    3.

    ProClust: improved clustering of protein sequences with an extended graph-based approach.

    Pipenbacher P, Schliep A, Schneckener S, Schönhuth A, Schomburg D, Schrader R.

    Bioinformatics. 2002;18 Suppl 2:S182-91.PMID: 12386002 [PubMed - indexed for MEDLINE]Related articlesFree article

    4.

    An integrated approach to the analysis and modeling of protein sequences and structures. III. A comparative study of sequence conservation in protein structural families using multiple structural alignments.

    Yang AS, Honig B.

    J Mol Biol. 2000 Aug 18;301(3):691-711.PMID: 10966778 [PubMed - indexed for MEDLINE]Related articles

    5.

    A sequence alignment-independent method for protein classification.

    Vries JK, Munshi R, Tobi D, Klein-Seetharaman J, Benos PV, Bahar I.

    Appl Bioinformatics. 2004;3(2-3):137-48.PMID: 15693739 [PubMed - indexed for MEDLINE]Related articles

    6.

    A word-oriented approach to alignment validation.

    Beiko RG, Chan CX, Ragan MA.

    Bioinformatics. 2005 May 15;21(10):2230-9. Epub 2005 Feb 22.PMID: 15728118 [PubMed - indexed for MEDLINE]Related articlesFree article

    7.

    HMM-ModE--improved classification using profile hidden Markov models by optimising the discrimination threshold and modifying emission probabilities with negative training sequences.

    Srivastava PK, Desai DK, Nandi S, Lynn AM.

    BMC Bioinformatics. 2007 Mar 27;8:104.PMID: 17389042 [PubMed - indexed for MEDLINE]Related articlesFree article

    8.

    Blast sampling for structural and functional analyses.

    Friedrich A, Ripp R, Garnier N, Bettler E, Deléage G, Poch O, Moulinier L.

    BMC Bioinformatics. 2007 Feb 23;8:62.PMID: 17319945 [PubMed - indexed for MEDLINE]Related articlesFree article

    9.

    The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction.

    Manning JR, Jefferson ER, Barton GJ.

    BMC Bioinformatics. 2008 Jan 25;9:51.PMID: 18221517 [PubMed - indexed for MEDLINE]Related articlesFree article

    10.

    Improved K-means clustering algorithm for exploring local protein sequence motifs representing common structural property.

    Zhong W, Altun G, Harrison R, Tai PC, Pan Y.

    IEEE Trans Nanobioscience. 2005 Sep;4(3):255-65.PMID: 16220690 [PubMed - indexed for MEDLINE]Related articles

    11.

    A comprehensive system for evaluation of remote sequence similarity detection.

    Qi Y, Sadreyev RI, Wang Y, Kim BH, Grishin NV.

    BMC Bioinformatics. 2007 Aug 28;8:314.PMID: 17725841 [PubMed - indexed for MEDLINE]Related articlesFree article

    12.

    DIALIGN-T: an improved algorithm for segment-based multiple sequence alignment.

    Subramanian AR, Weyer-Menkhoff J, Kaufmann M, Morgenstern B.

    BMC Bioinformatics. 2005 Mar 22;6:66.PMID: 15784139 [PubMed - indexed for MEDLINE]Related articlesFree article

    13.

    Subfamily logos: visualization of sequence deviations at alignment positions with high information content.

    Beitz E.

    BMC Bioinformatics. 2006 Jun 21;7:313.PMID: 16790056 [PubMed - indexed for MEDLINE]Related articlesFree article

    14.

    Accuracy of structure-based sequence alignment of automatic methods.

    Kim C, Lee B.

    BMC Bioinformatics. 2007 Sep 20;8:355.PMID: 17883866 [PubMed - indexed for MEDLINE]Related articlesFree article

    15.

    A new similarity measure among protein sequences.

    Wu KP, Lin HN, Sung TY, Hsu WL.

    Proc IEEE Comput Soc Bioinform Conf. 2003;2:347-52.PMID: 16452810 [PubMed - indexed for MEDLINE]Related articles

    16.

    Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation.

    Livingstone CD, Barton GJ.

    Comput Appl Biosci. 1993 Dec;9(6):745-56.PMID: 8143162 [PubMed - indexed for MEDLINE]Related articles

    17.

    Enhanced recognition of protein transmembrane domains with prediction-based structural profiles.

    Cao B, Porollo A, Adamczak R, Jarrell M, Meller J.

    Bioinformatics. 2006 Feb 1;22(3):303-9. Epub 2005 Nov 17.PMID: 16293670 [PubMed - indexed for MEDLINE]Related articlesFree article

    18.

    Simulated annealing algorithm for the multiple sequence alignment problem: the approach of polymers in a random medium.

    Hernández-Guía M, Mulet R, Rodríguez-Pérez S.

    Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Sep;72(3 Pt 1):031915. Epub 2005 Sep 27.PMID: 16241490 [PubMed - indexed for MEDLINE]Related articles

    19.

    Relation between weight matrix and substitution matrix: motif search by similarity.

    Zheng WM.

    Bioinformatics. 2005 Apr 1;21(7):938-43. Epub 2004 Oct 28.PMID: 15514002 [PubMed - indexed for MEDLINE]Related articlesFree article

    20.

    Gapped alignment of protein sequence motifs through Monte Carlo optimization of a hidden Markov model.

    Neuwald AF, Liu JS.

    BMC Bioinformatics. 2004 Oct 25;5:157.PMID: 15504234 [PubMed - indexed for MEDLINE]Related articlesFree article

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