Norman E Davey

Summary

Affiliation: European Molecular Biology Laboratory
Country: Germany

Publications

  1. pmc 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. doi request reprint 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. doi request reprint 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. pmc 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. pmc 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. doi request reprint 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. pmc 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. doi request reprint 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. doi request reprint 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
  10. ncbi request reprint 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 (Landmark Ed) 15:801-25. 2010

Collaborators

Detail Information

Publications25

  1. pmc 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. doi request reprint 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. doi request reprint 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. pmc 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. pmc 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. doi request reprint 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. pmc 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. doi request reprint 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
    ..Many input and search options are available, enabling a list of motifs to be compared to itself (to identify recurring motifs) or to datasets of known motifs...
  9. doi request reprint 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...
  10. ncbi request reprint 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 (Landmark Ed) 15:801-25. 2010
    ..g. of physical protein interactions) as input for computational discovery...
  11. pmc 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. pmc 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...
  13. pmc 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...
  14. pmc 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...
  15. pmc 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...
  16. doi request reprint 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
    ....
  17. doi request reprint 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
    ....
  18. doi request reprint The eukaryotic linear motif resource ELM: 10 years and counting
    Holger Dinkel
    Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, Department of Physiology, University of California, San Francisco, 600 16th Street, San Francisco, CA 94158, USA, Structural Studies Division, MRC, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK, Ruprecht Karls Universitat, 69117 Heidelberg, Germany, School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Co Dublin, Republic of Ireland, Laboratory of Bioinformatics and Biostatistics, Maria Sklodowska Curie Memorial Cancer Center and Institute of Oncology, WK Roentgena 5, 02 781 Warsaw, Poland, Protein Structure Function and Engineering Laboratory, Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires Consejo Nacional de Investigaciones Científicas y Técnicas Avenida Patricias Argentinas 435 CP 1405 Buenos Aires, Argentina and Departamento de Química Biológica and IQUIBICEN CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Gúiraldes 2160 CP 1428, Argentina
    Nucleic Acids Res 42:D259-66. 2014
    ..Furthermore, detailed information about motif-mediated interactions has been annotated and made available in standard exchange formats. Where appropriate, links are provided to resources such as switches.elm.eu.org and KEGG pathways. ..
  19. pmc Marked variability in the extent of protein disorder within and between viral families
    Ravindra Pushker
    UCD Complex and Adaptive Systems Laboratory, University College Dublin, Belfield, Dublin, Ireland
    PLoS ONE 8:e60724. 2013
    ..Differing disorder strategies are likely to impact on how different viruses modulate host factors, and on how rapidly viruses can evolve novel instances of SLiMs subverting host functions, such as innate and acquired immunity...
  20. doi request reprint 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...
  21. pmc 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...
  22. pmc 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...
  23. pmc 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...
  24. doi request reprint 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...
  25. pmc 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...