Research Topics
| Francesca DiellaSummaryAffiliation: European Molecular Biology Laboratory Country: Germany Publications
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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...- ELM--the database of eukaryotic linear motifsHolger 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... 
Attributes of short linear motifsNorman 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...- KEPE--a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factorsFrancesca Diella
Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
Bioinformatics 25:1-5. 2009..The KEPEmotif appears to be restricted to the metazoan lineage and has three length variants-short, medium and long-which do not appear to interchange... 
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...- Deciphering a global network of functionally associated post-translational modificationsPablo Minguez
Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
Mol Syst Biol 8:599. 2012..The global network of co-evolving PTM types implies a complex and intertwined post-translational regulation landscape that is likely to regulate multiple functional states of many if not all eukaryotic proteins... - Evidence for the concerted evolution between short linear protein motifs and their flanking regionsClaudia Chica
Structural and Computational Biology Unit, EMBL Heidelberg, Heidelberg, Germany
PLoS ONE 4:e6052. 2009..Sometimes linear motifs appear as isolated islands of conservation in multiple sequence alignments. However, they also occur in larger blocks of sequence conservation, suggesting an active role for the neighbouring amino acids... - 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)... - 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... - Phospho.ELM: a database of phosphorylation sites--update 2008Francesca Diella
Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
Nucleic Acids Res 36:D240-4. 2008..Phospho.ELM is available on line at: http://phospho.elm.eu.org... - Understanding eukaryotic linear motifs and their role in cell signaling and regulationFrancesca Diella
Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
Front Biosci 13:6580-603. 2008..The discrete deterministic properties implicit to these assemblies suggest that models for cell regulatory networks in systems biology should neither be overly dependent on stochastic nor on smooth deterministic approximations... - 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... - 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...