Rune Linding

Summary

Affiliation: European Molecular Biology Laboratory
Country: Germany

Publications

  1. pmc Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins
    Francesca Diella
    Cellzome AG, Heidelberg, Germany
    BMC Bioinformatics 5:79. 2004
  2. pmc GlobPlot: Exploring protein sequences for globularity and disorder
    Rune Linding
    European Molecular Biology Laboratory, Biocomputing Unit, D 69117 Heidelberg, Germany
    Nucleic Acids Res 31:3701-8. 2003
  3. ncbi request reprint Protein disorder prediction: implications for structural proteomics
    Rune Linding
    EMBL, Biocomputing Unit, Meyerhofstr 1, D 69117 Heidelberg, Germany
    Structure 11:1453-9. 2003
  4. 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
  5. pmc Systematic discovery of new recognition peptides mediating protein interaction networks
    Victor Neduva
    European Molecular Biology Laboratory, Heidelberg, Germany
    PLoS Biol 3:e405. 2005
  6. ncbi request reprint A comparative study of the relationship between protein structure and beta-aggregation in globular and intrinsically disordered proteins
    Rune Linding
    European Molecular Biology Laboratory, Programme for Structural and Computational biology, Meyerhofstr 1, D 69117 Heidelberg, Germany
    J Mol Biol 342:345-53. 2004
  7. pmc BLAST2SRS, a web server for flexible retrieval of related protein sequences in the SWISS-PROT and SPTrEMBL databases
    Konstantinos Bimpikis
    European Molecular Biology Laboratory, Postfach 10 2209, 69012 Heidelberg, Germany
    Nucleic Acids Res 31:3792-4. 2003
  8. doi request reprint Linear motif atlas for phosphorylation-dependent signaling
    Martin Lee Miller
    Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark
    Sci Signal 1:ra2. 2008
  9. pmc NetworKIN: a resource for exploring cellular phosphorylation networks
    Rune Linding
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
    Nucleic Acids Res 36:D695-9. 2008
  10. pmc Systematic discovery of in vivo phosphorylation networks
    Rune Linding
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
    Cell 129:1415-26. 2007

Collaborators

Detail Information

Publications16

  1. pmc Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins
    Francesca Diella
    Cellzome AG, Heidelberg, Germany
    BMC Bioinformatics 5:79. 2004
    ..The fast growing number of research reports on protein phosphorylation points to a general need for an accurate database dedicated to phosphorylation to provide easily retrievable information on phosphoproteins...
  2. pmc GlobPlot: Exploring protein sequences for globularity and disorder
    Rune Linding
    European Molecular Biology Laboratory, Biocomputing Unit, D 69117 Heidelberg, Germany
    Nucleic Acids Res 31:3701-8. 2003
    ..GlobPlot has a pipeline interface--GlobPipe--for the advanced user to do whole proteome analysis. GlobPlot can also be used as a generic infrastructure package for graphical displaying of any possible propensity...
  3. ncbi request reprint Protein disorder prediction: implications for structural proteomics
    Rune Linding
    EMBL, Biocomputing Unit, Meyerhofstr 1, D 69117 Heidelberg, Germany
    Structure 11:1453-9. 2003
    ..The tool is freely available via a web interface (http://dis.embl.de) and can be downloaded for use in large-scale studies...
  4. 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...
  5. pmc Systematic discovery of new recognition peptides mediating protein interaction networks
    Victor Neduva
    European Molecular Biology Laboratory, Heidelberg, Germany
    PLoS Biol 3:e405. 2005
    ..We estimate that there are dozens or even hundreds of linear motifs yet to be discovered that will give molecular insight into protein networks and greatly illuminate cellular processes...
  6. ncbi request reprint A comparative study of the relationship between protein structure and beta-aggregation in globular and intrinsically disordered proteins
    Rune Linding
    European Molecular Biology Laboratory, Programme for Structural and Computational biology, Meyerhofstr 1, D 69117 Heidelberg, Germany
    J Mol Biol 342:345-53. 2004
    ..Finally, we discuss the fact that although IDPs have a much lower aggregation propensity than globular proteins, this does not necessarily mean that they have a lower potential for amyloidosis...
  7. pmc BLAST2SRS, a web server for flexible retrieval of related protein sequences in the SWISS-PROT and SPTrEMBL databases
    Konstantinos Bimpikis
    European Molecular Biology Laboratory, Postfach 10 2209, 69012 Heidelberg, Germany
    Nucleic Acids Res 31:3792-4. 2003
    ..By allowing the user to control SRS from the BLAST output, BLAST2SRS (http://blast2srs.embl.de/) aims to meet this need. This server therefore combines the two ways to search sequence databases: similarity and keyword...
  8. doi request reprint Linear motif atlas for phosphorylation-dependent signaling
    Martin Lee Miller
    Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark
    Sci Signal 1:ra2. 2008
    ..The atlas is available as a community resource (http://netphorest.info)...
  9. pmc NetworKIN: a resource for exploring cellular phosphorylation networks
    Rune Linding
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
    Nucleic Acids Res 36:D695-9. 2008
    ..The database currently contains a predicted phosphorylation network with 20,224 site-specific interactions involving 3978 phosphoproteins and 73 human kinases from 20 families...
  10. pmc Systematic discovery of in vivo phosphorylation networks
    Rune Linding
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
    Cell 129:1415-26. 2007
    ..Applying this approach to DNA damage signaling, we show that 53BP1 and Rad50 are phosphorylated by CDK1 and ATM, respectively. We describe a scalable strategy to evaluate predictions, which suggests that BCLAF1 is a GSK-3 substrate...
  11. pmc ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins
    Pål Puntervoll
    Department of Molecular Biology, University of Bergen, Norway
    Nucleic Acids Res 31:3625-30. 2003
    ..Current filters are for cell compartment, globular domain clash and taxonomic range. In favourable cases, the filters can reduce the number of retained matches by an order of magnitude or more...
  12. pmc WW domains provide a platform for the assembly of multiprotein networks
    Robert J Ingham
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
    Mol Cell Biol 25:7092-106. 2005
    ..These data suggest that WW domains provide a versatile platform to link individual proteins into physiologically important networks...
  13. ncbi request reprint Normalization of nomenclature for peptide motifs as ligands of modular protein domains
    Rein Aasland
    Department of Molecular Biology, University of Bergen, 5020 Bergen, Norway
    FEBS Lett 513:141-4. 2002
    ..This proposal will be reviewed in the future and will therefore be open for the inclusion of new rules, modifications and changes...
  14. doi request reprint Directional and quantitative phosphorylation networks
    Claus Jørgensen
    Brief Funct Genomic Proteomic 7:17-26. 2008
    ..By combining quantitative measurements of phosphorylation events with computational approaches, we argue that systems level models will help to decipher complex diseases through the ability to predict cellular systems trajectories...
  15. doi request reprint Network medicine
    Tony Pawson
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Canada
    FEBS Lett 582:1266-70. 2008
    ..We term this approach, network medicine...
  16. pmc Phosphorylation networks regulating JNK activity in diverse genetic backgrounds
    Chris Bakal
    Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02215, USA
    Science 322:453-6. 2008
    ....