The DOI matches its Crossref record; 43 of the 43 references it cites were found in a registry or an index.
ELM--the database of eukaryotic linear motifs
Open accessAbstract
Linear motifs are short, evolutionarily plastic components of regulatory proteins and provide low-affinity interaction interfaces. These compact modules play central roles in mediating every aspect of the regulatory functionality of the cell. They are particularly prominent in mediating cell signaling, controlling protein turnover and directing protein localization. Given their importance, our understanding of motifs is surprisingly limited, largely as a result of the difficulty of discovery, both experimentally and computationally. The Eukaryotic Linear Motif (ELM) resource at http://elm.eu.org provides the biological community with a comprehensive database of known experimentally validated motifs, and an exploratory tool to discover putative linear motifs in user-submitted protein sequences. The current update of the ELM database comprises 1800 annotated motif instances representing 170 distinct functional classes, including approximately 500 novel instances and 24 novel classes. Several older motif class entries have been also revisited, improving annotation and adding novel instances. Furthermore, addition of full-text search capabilities, an enhanced interface and simplified batch download has improved the overall accessibility of the ELM data. 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.
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Cites
Dosztanyi, Z., Csizmok, V., Tompa, P., & Simon, I. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti541 · Cited by 1,960
Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs
Obenauer, J. C. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg584 · Cited by 1,596
SMART 6: recent updates and new developments
Letunic, I., Doerks, T., & Bork, P. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn808 · Cited by 956
Phospho.ELM: a database of phosphorylation sites--update 2011
Dinkel, H., Chica, C., Via, A., Gould, C. M., Jensen, L. J., Gibson, T. J., & Diella, F. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1104 · Cited by 740
Self-citationGain-of-function RAF1 mutations cause Noonan and LEOPARD syndromes with hypertrophic cardiomyopathy
Pandit, B., Sarkozy, A., Pennacchio, L. A., Carta, C., Oishi, K., Martinelli, S., Pogna, E. A., Schackwitz, W., Ustaszewska, A., Landstrom, A., et al. (2007) · Nature Genetics · doi:10.1038/ng2073 · Cited by 698
Protein phosphorylation in signaling – 50 years and counting
Pawson, T., & Scott, J. D. (2005) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2005.04.013 · Cited by 694
Hermjakob, H., Montecchi-Palazzi, L., Bader, G., Wojcik, J., Salwinski, L., Ceol, A., Moore, S., Orchard, S., Sarkans, U., von Mering, C., et al. (2004) · Nature Biotechnology · doi:10.1038/nbt926 · Cited by 630
Attributes of short linear motifs
Davey, N. E., Van Roey, K., Weatheritt, R. J., Toedt, G., Uyar, B., Altenberg, B., Budd, A., Diella, F., Dinkel, H., & Gibson, T. J. (2011) · Molecular BioSystems · doi:10.1039/c1mb05231d · Cited by 628
Self-citationELM server: a new resource for investigating short functional sites in modular eukaryotic proteins
Puntervoll, P. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg545 · Cited by 602
Transient Protein-Protein Interactions: Structural, Functional, and Network Properties
Perkins, J. R., Diboun, I., Dessailly, B. H., Lees, J. G., & Orengo, C. (2010) · Structure · doi:10.1016/j.str.2010.08.007 · Cited by 520
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Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing
Yang, X., Coulombe-Huntington, J., Kang, S., Sheynkman, G. M., Hao, T., Richardson, A., Sun, S., Yang, F., Shen, Y. A., Murray, R. R., et al. (2016) · Cell · doi:10.1016/j.cell.2016.01.029 · Cited by 583
Viral dark matter and virus–host interactions resolved from publicly available microbial genomes
Roux, S., Hallam, S. J., Woyke, T., & Sullivan, M. B. (2015) · eLife · doi:10.7554/elife.08490 · Cited by 478
Bujalka, H., Koenning, M., Jackson, S., Perreau, V. M., Pope, B., Hay, C. M., Mitew, S., Hill, A. F., Lu, Q. R., Wegner, M., et al. (2013) · PLoS Biology · doi:10.1371/journal.pbio.1001625 · Cited by 271
“The UniProt mouse MYRF sequence (accession number Q3UR85) was submitted to several subcellular targeting motif and feature predictors including ELM [46], PSORTII [47], NucPred [48], TMPRED [49], HMMTOP [50], Das-TMfilter [51], Toppred II [52], Paircoil2 [53], and to the protein databases PFAM [54] and Prosite [55].”
MethodIvarsson, Y., Arnold, R., McLaughlin, M., Nim, S., Joshi, R., Ray, D., Liu, B., Teyra, J., Pawson, T., Moffat, J., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1312296111 · Cited by 135
Goldman, A., Roy, J., Bodenmiller, B., Wanka, S., Landry, C. R., Aebersold, R., & Cyert, M. S. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.05.012 · Cited by 109
Metadata
- Authors
- Dinkel, H., Michael, S., Weatheritt, R. J., Davey, N. E., Van Roey, K., Altenberg, B., Toedt, G., Uyar, B., Seiler, M., Budd, A., Jodicke, L., Dammert, M. A., Schroeter, C., Hammer, M., Schmidt, T., Jehl, P., McGuigan, C., Dymecka, M., Chica, C., Luck, K., Via, A., Chatr-aryamontri, A., Haslam, N., Grebnev, G., Edwards, R. J., Steinmetz, M. O., Meiselbach, H., Diella, F., & Gibson, T. J.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2011-11-21
- Volume
- 40
- Issue
- D1
- Pages
- D242-D251
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2143593035
- Cited by
- 438
- References
- 43
- FWCI
- 22.57
- Type
- journal article
- Language
- en
- Open access
- gold
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- Dinkel, H., Michael, S., Weatheritt, R. J., Davey, N. E., Van Roey, K., Altenberg, B., Toedt, G., Uyar, B., Seiler, M., Budd, A., Jodicke, L., Dammert, M. A., Schroeter, C., Hammer, M., Schmidt, T., Jehl, P., McGuigan, C., Dymecka, M., Chica, C., . . . Gibson, T. J. (2012). ELM--the database of eukaryotic linear motifs. Nucleic Acids Research. https://doi.org/10.1093/nar/gkr1064
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
