Sequence-based feature prediction and annotation of proteins
暂无分享,去创建一个
M. Tress | A. Valencia | P. Bork | C. Ouzounis | A. S. Juncker | S. Brunak | L. Jensen | G. von Heijne | R. Casadio | Andreas Bernsel | A. Pierleoni | L. Jensen
[1] G von Heijne,et al. Patterns of amino acids near signal-sequence cleavage sites. , 1983, European journal of biochemistry.
[2] G von Heijne,et al. Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. , 1992, Journal of molecular biology.
[3] U. Hobohm,et al. Enlarged representative set of protein structures , 1994, Protein science : a publication of the Protein Society.
[4] S. Brunak,et al. Defining a similarity threshold for a functional protein sequence pattern: The signal peptide cleavage site , 1996, Proteins.
[5] Thomas L. Madden,et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.
[6] S. Brunak,et al. SHORT COMMUNICATION Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites , 1997 .
[7] Peter D. Karp,et al. Prediction of Enzyme Classification from Protein Sequence without the Use of Sequence Similarity , 1997, ISMB.
[8] Chris Sander,et al. EUCLID: automatic classification of proteins in functional classes by their database annotations , 1998, Bioinform..
[9] M. Riley. Systems for categorizing functions of gene products. , 1998, Current Opinion in Structural Biology.
[10] D T Jones,et al. Protein secondary structure prediction based on position-specific scoring matrices. , 1999, Journal of molecular biology.
[11] N. Blom,et al. Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. , 1999, Journal of molecular biology.
[12] A. Valencia,et al. Practical limits of function prediction , 2000, Proteins.
[13] Pierre Baldi,et al. Assessing the accuracy of prediction algorithms for classification: an overview , 2000, Bioinform..
[14] Keith F. Tipton,et al. History of the enzyme nomenclature system , 2000, Bioinform..
[15] M. Ashburner,et al. Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.
[16] A. Krogh,et al. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. , 2001, Journal of molecular biology.
[17] István Simon,et al. The HMMTOP transmembrane topology prediction server , 2001, Bioinform..
[18] Annabel E. Todd,et al. Evolution of function in protein superfamilies, from a structural perspective. , 2001, Journal of molecular biology.
[19] C. A. Andersen,et al. Prediction of human protein function from post-translational modifications and localization features. , 2002, Journal of molecular biology.
[20] Burkhard Rost,et al. Sequence conserved for subcellular localization , 2002, Protein science : a publication of the Protein Society.
[21] Anton J. Enright,et al. Classification schemes for protein structure and function , 2003, Nature Reviews Genetics.
[22] Søren Brunak,et al. Prediction of human protein function according to Gene Ontology categories , 2003, Bioinform..
[23] A. Krogh,et al. Reliability measures for membrane protein topology prediction algorithms. , 2003, Journal of molecular biology.
[24] Michael B. Yaffe,et al. Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs , 2003, Nucleic Acids Res..
[25] N. Blom,et al. Prediction of post‐translational glycosylation and phosphorylation of proteins from the amino acid sequence , 2004, Proteomics.
[26] Janet M. Thornton,et al. The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data , 2004, Nucleic Acids Res..
[27] A. Elofsson,et al. Best α‐helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information , 2004 .
[28] S. Brunak,et al. Improved prediction of signal peptides: SignalP 3.0. , 2004, Journal of molecular biology.
[29] Erik L. L. Sonnhammer,et al. An HMM posterior decoder for sequence feature prediction that includes homology information , 2005, ISMB.
[30] Walter R. Gilks,et al. Probabilistic annotation of protein sequences based on functional classifications , 2005, BMC Bioinformatics.
[31] D. Eisenberg,et al. Inference of protein function from protein structure. , 2005, Structure.
[32] S. Brunak,et al. Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites. , 2005, Glycobiology.
[33] Daisuke Kihara,et al. Enhanced automated function prediction using distantly related sequences and contextual association by PFP , 2006, Protein science : a publication of the Protein Society.
[34] M. Resh,et al. Trafficking and signaling by fatty-acylated and prenylated proteins , 2006, Nature chemical biology.
[35] Arne Elofsson,et al. PONGO: a web server for multiple predictions of all-alpha transmembrane proteins , 2006, Nucleic Acids Res..
[36] Yu Xue,et al. CSS-Palm: palmitoylation site prediction with a clustering and scoring strategy (CSS) , 2006, Bioinform..
[37] Erik Granseth,et al. Structural classification and prediction of reentrant regions in alpha-helical transmembrane proteins: application to complete genomes. , 2006, Journal of molecular biology.
[38] John F. Antoniw,et al. A combinatorial pattern discovery approach for the prediction of membrane dipping (re-entrant) loops , 2006, ISMB.
[39] Piero Fariselli,et al. BaCelLo: a balanced subcellular localization predictor , 2006, ISMB.
[40] Paul Horton,et al. Nucleic Acids Research Advance Access published May 21, 2007 WoLF PSORT: protein localization predictor , 2007 .
[41] J. Ferrell,et al. Mechanisms of specificity in protein phosphorylation , 2007, Nature Reviews Molecular Cell Biology.
[42] Christian von Mering,et al. STRING 7—recent developments in the integration and prediction of protein interactions , 2006, Nucleic Acids Res..
[43] Alfonso Valencia,et al. firestar—prediction of functionally important residues using structural templates and alignment reliability , 2007, Nucleic Acids Res..
[44] Walter R. Gilks,et al. CORRIE: enzyme sequence annotation with confidence estimates , 2007, BMC Bioinformatics.
[45] David T. Jones,et al. Improving the accuracy of transmembrane protein topology prediction using evolutionary information , 2007, Bioinform..
[46] P. Bork,et al. Systematic Discovery of In Vivo Phosphorylation Networks , 2007, Cell.
[47] K. Julenius. NetCGlyc 1.0: prediction of mammalian C-mannosylation sites. , 2007, Glycobiology.
[48] S. Brunak,et al. Locating proteins in the cell using TargetP, SignalP and related tools , 2007, Nature Protocols.
[49] Birgit Eisenhaber,et al. Posttranslational modifications and subcellular localization signals: indicators of sequence regions without inherent 3D structure? , 2007, Current protein & peptide science.
[50] Xin Chen,et al. FragAnchor: A Large-Scale Predictor of Glycosylphosphatidylinositol Anchors in Eukaryote Protein Sequences by Qualitative Scoring , 2007, Genom. Proteom. Bioinform..
[51] Shuli Kang,et al. Meta-prediction of phosphorylation sites with weighted voting and restricted grid search parameter selection , 2008, Nucleic acids research.
[52] P. Bork,et al. Linear Motif Atlas for Phosphorylation-Dependent Signaling , 2008, Science Signaling.
[53] Pier Luigi Martelli,et al. PredGPI: a GPI-anchor predictor , 2008, BMC Bioinformatics.
[54] Michael J. E. Sternberg,et al. ConFunc - functional annotation in the twilight zone , 2008, Bioinform..
[55] E. Birney,et al. Pfam: the protein families database , 2013, Nucleic Acids Res..
[56] Andreas Prlic,et al. The Protein Feature Ontology: a tool for the unification of protein feature annotations , 2008, Bioinform..
[57] Christine A. Orengo,et al. FFPred: an integrated feature-based function prediction server for vertebrate proteomes , 2008, Nucleic Acids Res..
[58] P. Bork,et al. Predicting biological networks from genomic data , 2008, FEBS letters.
[59] L. Holm,et al. The Pfam protein families database , 2005, Nucleic Acids Res..