Nucleic Acids Research, 2003, Vol. 31, No. 13 3625-3630
© 2003 Oxford University Press
ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins
Department of Molecular Biology, University of Bergen, Norway 1 European Molecular Biology Laboratory, Postfach 10.2209, 69012 Heidelberg, Germany 2 Division of Biological Chemistry and Molecular Microbiology, University of Dundee, Dundee, UK 3 Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Rome, Italy 4 Cellzome AG, Heidelberg, Germany 5 BioInfoBank Institute, Poznan, Poland
*To whom correspondence should be addressed. Tel: +49 6221387398; Fax: +49 6221387517; Email: toby.gibson{at}embl.de
The authors wish it to be known that, in their opinion, the first three authors should be regarded as joint First Authors.
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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J. D. Aroca-Aguilar, F. Sanchez-Sanchez, S. Ghosh, M. Coca-Prados, and J. Escribano Myocilin Mutations Causing Glaucoma Inhibit the Intracellular Endoproteolytic Cleavage of Myocilin between Amino Acids Arg226 and Ile227 J. Biol. Chem., June 3, 2005; 280(22): 21043 - 21051. [Abstract] [Full Text] [PDF]
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S. K. Patnaik and P. Stanley Mouse Large Can Modify Complex N- and Mucin O-Glycans on {alpha}-Dystroglycan to Induce Laminin Binding J. Biol. Chem., May 27, 2005; 280(21): 20851 - 20859. [Abstract] [Full Text] [PDF]
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D. Plewczynski, A. Tkacz, L. S. Wyrwicz, and L. Rychlewski AutoMotif server: prediction of single residue post-translational modifications in proteins Bioinformatics, May 15, 2005; 21(10): 2525 - 2527. [Abstract] [Full Text] [PDF]
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T. M. W. Nye, C. Berzuini, W. R. Gilks, M. M. Babu, and S. A. Teichmann Statistical analysis of domains in interacting protein pairs Bioinformatics, April 1, 2005; 21(7): 993 - 1001. [Abstract] [Full Text] [PDF]
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F. Ferre, G. Ausiello, A. Zanzoni, and M. Helmer-Citterich SURFACE: a database of protein surface regions for functional annotation Nucleic Acids Res., January 1, 2004; 32(90001): D240 - 244. [Abstract] [Full Text] [PDF]
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J.-J. Shieh, C.-J. Pan, B. C. Mansfield, and J. Y. Chou A Glucose-6-phosphate Hydrolase, Widely Expressed Outside the Liver, Can Explain Age-dependent Resolution of Hypoglycemia in Glycogen Storage Disease Type Ia J. Biol. Chem., November 21, 2003; 278(47): 47098 - 47103. [Abstract] [Full Text] [PDF]
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R. Nair and B. Rost LOC3D: annotate sub-cellular localization for protein structures Nucleic Acids Res., July 1, 2003; 31(13): 3337 - 3340. [Abstract] [Full Text] [PDF]
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R. Linding, R. B. Russell, V. Neduva, and T. J. Gibson GlobPlot: exploring protein sequences for globularity and disorder Nucleic Acids Res., July 1, 2003; 31(13): 3701 - 3708. [Abstract] [Full Text] [PDF]
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C. Ramu SIRW: a web server for the Simple Indexing and Retrieval System that combines sequence motif searches with keyword searches Nucleic Acids Res., July 1, 2003; 31(13): 3771 - 3774. [Abstract] [Full Text] [PDF]
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