Norman E Davey

Summary

Affiliation: European Molecular Biology Laboratory
Country: Germany

Publications

  1. ncbi SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions
    Norman E Davey
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Baden Württemberg 69117, Germany
    Nucleic Acids Res 40:10628-41. 2012
  2. ncbi How viruses hijack cell regulation
    Norman E Davey
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
    Trends Biochem Sci 36:159-69. 2011
  3. ncbi Attributes of short linear motifs
    Norman E Davey
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Biosyst 8:268-81. 2012
  4. ncbi Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins
    Norman E Davey
    UCD Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Ireland
    BMC Bioinformatics 11:14. 2010
  5. ncbi SLiMFinder: a probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins
    Richard J Edwards
    University College Dublin Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Ireland
    PLoS ONE 2:e967. 2007
  6. ncbi Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery
    Norman E Davey
    UCD Complex and Adaptive Systems Laboratory, UCD Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland
    Bioinformatics 25:443-50. 2009
  7. ncbi ELM--the database of eukaryotic linear motifs
    Holger Dinkel
    Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
    Nucleic Acids Res 40:D242-51. 2012
  8. ncbi CompariMotif: quick and easy comparisons of sequence motifs
    Richard J Edwards
    UCD Complex and Adaptive Systems Laboratory and UCD Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland
    Bioinformatics 24:1307-9. 2008
  9. ncbi Computational identification and analysis of protein short linear motifs
    Norman E Davey
    UCD Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Ireland
    Front Biosci 15:801-25. 2010
  10. ncbi SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs
    Norman E Davey
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
    Nucleic Acids Res 38:W534-9. 2010

Collaborators

Detail Information

Publications23

  1. ncbi SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions
    Norman E Davey
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Baden Württemberg 69117, Germany
    Nucleic Acids Res 40:10628-41. 2012
    ..Finally, the human proteome is analysed to create a set of highly conserved putative motif instances, including a novel site on translation initiation factor eIF2A that may regulate translation through binding of eIF4E...
  2. ncbi How viruses hijack cell regulation
    Norman E Davey
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
    Trends Biochem Sci 36:159-69. 2011
    ....
  3. ncbi Attributes of short linear motifs
    Norman E Davey
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Biosyst 8:268-81. 2012
    ..Finally, the most interesting conclusions are examined in regard to their functional consequences...
  4. ncbi Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins
    Norman E Davey
    UCD Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Ireland
    BMC Bioinformatics 11:14. 2010
    ..Here, we develop more exact methods and explore the potential biases of computationally efficient approximations...
  5. ncbi SLiMFinder: a probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins
    Richard J Edwards
    University College Dublin Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Ireland
    PLoS ONE 2:e967. 2007
    ..Incorporating ambiguous amino acid positions and/or variable-length wildcard spacers between defined residues further complicates the matter...
  6. ncbi Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery
    Norman E Davey
    UCD Complex and Adaptive Systems Laboratory, UCD Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland
    Bioinformatics 25:443-50. 2009
    ..Their short and degenerate nature presents a challenge for computational discovery. We sought to improve SLiM discovery by incorporating evolutionary information, since SLiMs are more conserved than surrounding residues...
  7. ncbi ELM--the database of eukaryotic linear motifs
    Holger Dinkel
    Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
    Nucleic Acids Res 40:D242-51. 2012
    ..The motif discovery portion of the ELM resource has added conservation, and structural attributes have been incorporated to aid users to discriminate biologically relevant motifs from stochastically occurring non-functional instances...
  8. ncbi CompariMotif: quick and easy comparisons of sequence motifs
    Richard J Edwards
    UCD Complex and Adaptive Systems Laboratory and UCD Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland
    Bioinformatics 24:1307-9. 2008
    ..ucd.ie/ and is freely available for academic use as a set of open source Python modules under a GNU General Public License from http://bioinformatics.ucd.ie/shields/software/comparimotif/..
  9. ncbi Computational identification and analysis of protein short linear motifs
    Norman E Davey
    UCD Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Ireland
    Front Biosci 15:801-25. 2010
    ..g. of physical protein interactions) as input for computational discovery...
  10. ncbi SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs
    Norman E Davey
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
    Nucleic Acids Res 38:W534-9. 2010
    ..Returned motifs can also be compared with known SLiMs from the literature using CompariMotif. All results are available for download. The SLiMFinder server is available at: http://bioware.ucd.ie/slimfinder.html...
  11. ncbi The SLiMDisc server: short, linear motif discovery in proteins
    Norman E Davey
    UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
    Nucleic Acids Res 35:W455-9. 2007
    ..Returned motifs can also be compared with known SLiMs from the literature. SLiMDisc is available at: http://bioware.ucd.ie/~slimdisc/...
  12. ncbi SLiMSearch 2.0: biological context for short linear motifs in proteins
    Norman E Davey
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
    Nucleic Acids Res 39:W56-60. 2011
    ..Users can search motifs against the human proteome or a subset thereof defined by Uniprot accession numbers or GO term. The SLiMSearch server is available at: http://bioware.ucd.ie/slimsearch2.html...
  13. ncbi Protein disorder and short conserved motifs in disordered regions are enriched near the cytoplasmic side of single-pass transmembrane proteins
    Ilias Stavropoulos
    School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
    PLoS ONE 7:e44389. 2012
    ..We conclude that elevated disorder within the cytoplasmic tail of many transmembrane proteins is likely to be associated with enrichment for signalling interactions mediated by conserved short motifs...
  14. ncbi ELM: the status of the 2010 eukaryotic linear motif resource
    Cathryn M Gould
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 38:D167-80. 2010
    ..Using the links, researchers can explore the motifs, proteins, complex structures and associated literature to evaluate whether candidate motifs might be worth experimental investigation...
  15. ncbi Motif switches: decision-making in cell regulation
    Kim Van Roey
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Curr Opin Struct Biol 22:378-85. 2012
    ....
  16. ncbi Structure of the immature retroviral capsid at 8 Å resolution by cryo-electron microscopy
    Tanmay A M Bharat
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nature 487:385-9. 2012
    ....
  17. ncbi The switches.ELM Resource: A Compendium of Conditional Regulatory Interaction Interfaces
    Kim Van Roey
    Structural and Computational Biology Unit, European Molecular Biology Laboratory EMBL, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Sci Signal 6:rs7. 2013
    ..We foresee switches.ELM complementing available resources to extend our knowledge of the molecular mechanisms underlying cell signaling...
  18. ncbi Web server to identify similarity of amino acid motifs to compounds (SAAMCO)
    Fergal P Casey
    UCD Conway Institute of Biomolecular and Biomedical Sciences and Complex and Adaptive Systems Laboratory CASL, University College Dublin, Dublin, Ireland
    J Chem Inf Model 48:1524-9. 2008
    ..The tabulated results can be analyzed by linking to appropriate databases and by visualization...
  19. ncbi SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent
    Norman E Davey
    Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland
    Nucleic Acids Res 34:3546-54. 2006
    ..An implementation of Multiple Spanning Tree weighting outperformed two other weighting schemes, in a variety of settings...
  20. ncbi Linear motifs confer functional diversity onto splice variants
    Robert J Weatheritt
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg 69117, Germany
    Nucleic Acids Res 40:7123-31. 2012
    ..This study, therefore, demonstrates that short linear motifs are key components for establishing protein diversity between splice variants...
  21. ncbi Conserved and variable features of Gag structure and arrangement in immature retrovirus particles
    Alex De Marco
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    J Virol 84:11729-36. 2010
    ..We conclude that the arrangement of the structural domains of CA is well conserved across genera, whereas the relationship between CA, the spacer peptide region, and the nucleic acid is more specific to each genus...
  22. ncbi Insights into RNA biology from an atlas of mammalian mRNA-binding proteins
    Alfredo Castello
    European Molecular Biology Laboratory, Heidelberg, Germany
    Cell 149:1393-406. 2012
    ..Interactome capture is broadly applicable to study mRNA interactome composition and dynamics in varied biological settings...
  23. ncbi Properties of the adeno-associated virus assembly-activating protein
    Matthias Naumer
    German Cancer Research Center, Research Program Infection and Cancer, Heidelberg, Germany
    J Virol 86:13038-48. 2012
    ..Combined, these observations suggest a possible scaffolding activity of AAP in the AAV capsid assembly reaction...