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ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins - PubMed

  • ️Wed Jan 01 2003

ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins

Pål Puntervoll et al. Nucleic Acids Res. 2003.

Abstract

Multidomain proteins predominate in eukaryotic proteomes. Individual functions assigned to different sequence segments combine to create a complex function for the whole protein. While on-line resources are available for revealing globular domains in sequences, there has hitherto been no comprehensive collection of small functional sites/motifs comparable to the globular domain resources, yet these are as important for the function of multidomain proteins. Short linear peptide motifs are used for cell compartment targeting, protein-protein interaction, regulation by phosphorylation, acetylation, glycosylation and a host of other post-translational modifications. ELM, the Eukaryotic Linear Motif server at http://elm.eu.org/, is a new bioinformatics resource for investigating candidate short non-globular functional motifs in eukaryotic proteins, aiming to fill the void in bioinformatics tools. Sequence comparisons with short motifs are difficult to evaluate because the usual significance assessments are inappropriate. Therefore the server is implemented with several logical filters to eliminate false positives. 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.

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Figures

Figure 1
Figure 1

Scheme of the ELM server flowthrough using human RASN as a query. Dashed boxes indicate the four stages from input to result. As the server is further developed, more filters will be added (light blue) requiring more query-dependent data to be retrievable (pink parallelograms).

Figure 2
Figure 2

Example of ELM server output using a short sequence, human RASN, as query. The output provides a table summarising the matches and the filtering, a list of globular domains revealed by the SMART server (in this case the RAS domain entry), the list of motif matches that survived filtering (in this case only the C-terminal prenylation site), and finally the list of matches excluded by domain filtering. Hyperlinks to the filtered results as well as to ELM annotation are provided.

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