Research Topics
| Rune LindingSummaryAffiliation: European Molecular Biology Laboratory Country: Germany Publications
| Collaborators
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Detail Information
Publications
Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteinsFrancesca 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...- GlobPlot: Exploring protein sequences for globularity and disorderRune 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... 
Protein disorder prediction: implications for structural proteomicsRune 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...- ELM: the status of the 2010 eukaryotic linear motif resourceCathryn 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... - Systematic discovery of new recognition peptides mediating protein interaction networksVictor 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... - A comparative study of the relationship between protein structure and beta-aggregation in globular and intrinsically disordered proteinsRune 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... - BLAST2SRS, a web server for flexible retrieval of related protein sequences in the SWISS-PROT and SPTrEMBL databasesKonstantinos 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... 
Linear motif atlas for phosphorylation-dependent signalingMartin 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)...- NetworKIN: a resource for exploring cellular phosphorylation networksRune 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... - Systematic discovery of in vivo phosphorylation networksRune 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... - ELM server: A new resource for investigating short functional sites in modular eukaryotic proteinsPål 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... - WW domains provide a platform for the assembly of multiprotein networksRobert 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... - Normalization of nomenclature for peptide motifs as ligands of modular protein domainsRein 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... - Directional and quantitative phosphorylation networksClaus 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... - Network medicineTony Pawson
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Canada
FEBS Lett 582:1266-70. 2008..We term this approach, network medicine... - Phosphorylation networks regulating JNK activity in diverse genetic backgroundsChris Bakal
Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02215, USA
Science 322:453-6. 2008....