The ELM project is/was funded by:
- The Quality of Life and Management of Living Resources programme, The European Commission Community Research.
- The EMBRACE Network of Excellence.
- Become an ELM sponsor?
The ELM logo was designed by:
Hosting:We are very grateful to the people at EU.org for providing the elm.eu.org domain for free.
The ELM project is powered by:
The ELM server
ELM is a computational biology resource for investigating candidate functional sites in eukaryotic proteins. Functional sites which fit to the description "linear motif" are currently specified as patterns using Regular Expression rules. To improve the predictive power, context-based rules and logical filters are being developed and applied to reduce the amount of false positives.
The current version of the ELM server provides core functionality including filtering by cell compartment, phylogeny, globular domain clash (using the SMART/Pfam databases) and structure. In addition, both the known ELM instances and any positionally conserved matches in sequences similar to ELM instance sequences are identified and displayed (see ELM instance mapper). Although the ELM resource contains a large collection of functional site motifs, the current set of motifs is not exhaustive.
Experimental detection of short regulatory motifs in eukaryotic proteins: tips for good practice as well as for bad
Gibson TJ, Dinkel H, Van Roey K, Diella F, (2015) Cell Communication & Signaling.
Proteome-wide analysis of human disease mutations in short linear motifs: neglected players in cancer?
Uyar B, Weatheritt RJ, Dinkel H, Davey NE, Gibson TJ, (2014) Mol Biosyst.
Short Linear Motifs: Ubiquitous and Functionally Diverse Protein Interaction Modules Directing Cell Regulation
Van Roey K, Uyar B, Weatheritt RJ, Dinkel H, Seiler M, Budd A, Gibson TJ, Davey NE. (2014) Chem Rev. 2014 Jun 13.
The eukaryotic linear motif resource ELM: 10 years and counting
Dinkel H, Van Roey K, Michael S, Davey NE, Weatheritt RJ, Born D, Speck T, Krüger D, Grebnev G, Kuban M, Strumillo M, Uyar B, Budd A, Altenberg B, Seiler M, Chemes LB, Glavina J, Sánchez IE, Diella F, Gibson TJ. (2014) Nucleic Acids Res., Nov, 2013
The switches.ELM Resource: A Compendium of Conditional Regulatory Interaction Interfaces
Van Roey K, Dinkel H, Weatheritt RJ, Gibson TJ, Davey ND. (2013). Sci. Signal., 2013 April
iELM - a web server to explore short linear motif-mediated interactions.
Weatheritt RJ, Jehl P, Dinkel H, Gibson TJ. (2012). Nucleic Acids Res. 2012 Jul
ELM - the database of eukaryotic linear motifs
Dinkel H, Michael S, Weatheritt RJ, Davey NE, Roey K, Altenberg B, Toedt G, Uyar B, Seiler M, Budd A, Joedicke L, Dammert M, 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 RJ, Steinmetz MO, Meiselbach H, Diella F, and Gibson TJ (2012). Nucleic Acids Res 2011 Nov 21
Attributes of short linear motifs.
Davey NE, Van Roey K, Weatheritt RJ, Toedt G, Uyar B, Altenberg B, Budd A, Diella F, Dinkel H, Gibson TJ. (2011). Mol Biosyst. 2011 Sep 12.
ELM: the status of the 2010 eukaryotic linear motif resource
Gould, C M, Diella, F, Via, A, Puntervoll, P, Gemünd, C, Chabanis-Davidson, S, Michael, S, Sayadi, A, Bryne, J C, Chica, C, Seiler, M, Davey, N E, Haslam, N, Weatheritt, R J, Budd, A, Hughes, T, Pas, J, Rychlewski, L, Travè, G, Aasland, R, Helmer-Citterich, M, Linding, R, Gibson, T J. (2009). Nucleic Acids Res 2009 Nov 17
A structure filter for the Eukaryotic Linear Motif Resource.
Via A., Gould CM., Gemünd C., Gibson T.J., Helmer-Citterich M. (2009) BMC Bioinformatics, 24;10:351.
Understanding eukaryotic linear motifs and their role in cell signaling and regulation
Diella, F., Haslam, N., Chica, N., Budd, A., Michael, S., Brown, N. P., Trave, G., Gibson, T.J. (2009). Frontiers in Bioscience 13, 6580-6603
A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences.
Chica C., Labarga A., Gould CM., Lopez R., Gibson T.J. (2008). BMC Bioinformatics, 6;9:229.
ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins.
Puntervoll, P., Linding, R., Gemünd, C., Chabanis-Davidson, S., Mattingsdal, M., Cameron, S., Martin, D. M. A., Ausiello, G., Brannetti, B., Costantini, A., Ferrè, F., Maselli, V., Via, A., Cesareni, G., Diella, F., Superti-Furga, G., Wyrwicz, L., Ramu, C., McGuigan, C., Gudavalli, R., Letunic, I., Bork, P., Rychlewski, L., Küster, B., Helmer-Citterich, M., Hunter, W. N., Aasland, R., & Gibson, T.J. (2003). Nucleic Acids Res., 31: 3625-3630.
External tools used:
IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content.
Dosztányi Z, Csizmók V, Tompa P, Simon I.
Bioinformatics. 2005 Aug 15;21(16):3433-4. Epub 2005 Jun 14. 15955779
SMART 6: recent updates and new developments.
Letunic I, Doerks T, Bork P.
Nucleic Acids Res. 2009 Jan;37:D229-32. Epub 2008 Oct 31. 18978020
The Pfam protein families database.
Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer EL, Eddy SR, Bateman A. Nucleic Acids Res. 2010 Jan;38(Database issue):D211-22. Epub 2009 Nov 17. 19920124
GlobPlot: Exploring protein sequences for globularity and disorder.
Linding R, Russell RB, Neduva V, Gibson TJ.
Nucleic Acids Res. 2003 Jul 1;31(13):3701-8. 12824398
Phospho.ELM: a database of phosphorylation sites - update 2011.
Dinkel H, Chica C, Via A, Gould CM, Jensen LJ, Gibson TJ, Diella F.
Nucleic Acids Res. 2011 Jan;39(Database issue):D261-7. Epub 2010 Nov 9. 21062810
Cell regulation: determined to signal discrete cooperation
Gibson, T.J. (2009). Trends Biochem Sci., 34(10): 471-82
The ELM consortium involves five European academic institutions (EMBL Heidelberg, University of Rome/Tor Vergata, University of Bergen, University of Dundee, and the BioInfoBank Institute) and one biotechnology company (CellZome GmbH), and was funded by EU. Here is a list of current and previous annotators and contributors of ELM:
D-69117 Heidelberg, Germany
Toby Gibson's group is in the Biocomputing Unit at the European Molecular Biology Laboratory (EMBL). Toby is the coordinator of the ELM Consortium. Holger Dinkel is responsible for software development, server maintenance and the visual representations.
- Brigitte Altenberg-Greulich
- Peer Bork
- Nigel Brown
- Aidan Budd
- Sophie Chabanis-Davidson
- Claudia Chica
- Victoria Damerell
- Norman Davey
- Francesca Diella
- Holger Dinkel
- Christine Gemünd
- Toby Gibson
- Kate Gould
- Rambabu Gudavalli
- Peter Jehl
- Arne Knudsen
- Helen Kühn
- Manjeet Kumar
- Ivica Letunic
- Rune Linding
- Katja Luck
- Caroline McGuigan
- Sushama Michael
- Chenna Ramu
- Markus Seiler
- Tobias Speck
- Vera Thiel
- Grischa Toedt
- Bora Uyar
- Kim van Roey
- Robert Weatheritt
Via della Ricerca Scientifica,
00133 Rome, Italy
The Centre for Molecular Bioinformatics of the Department of Biology at the University of Rome Tor Vergata is involved in the development of computational tools for the study of protein interaction and structure-function relationships.
- Gabriele Ausiello
- Barbara Brannetti
- Gianni Cesareni
- Anna Costantini
- Fabrizio Ferrè
- Manuela Helmer Citteric
- Vincenza Maselli
- Simona Panni
- Livia Perfetto
- Ahmed Sayadi
- Allegra Via
- Andreas Zanzoni
N-5020 Bergen, Norway
The field of interest of the group of Rein Aasland at the Department of Molecular Biology, University of Bergen is the influence of chromatin on gene expression. The Bergen team is responsible for siteseeing and informatics on functional sites in nuclear proteins.
- Rein Aasland
- Jan Christian Bryne
- Tim Hughes
- Morten Mattingsdal
- Pal Puntervoll
- Prakash Yalamanchili
DD1 5EH Dundee, Scotland UK
- Scott Cameron
- William Hunter
- David Martin
D-69117 Heidelberg, Germany
CellZome is a functional genomics company. Giulio Superti-Furga is the ELM partner whose research interests are in tyrosine phosphoylation.
- Bernhard Kuester
- Gulio Superti-Furga
60-744 Poznan, Poland
The main expertise of the BioInfo.PL group, headed by Leszek Rychlewski, is the development of protein structure prediction methods. The group will be responsible for adding an experimental ab initio filter to the ELM pipeline.
- Krzysztof Ginalski
- Marcin Grotthuss, von
- Andrzej Kierzek
- Jakub Pas
- Leszek Rychlewski
- Lucjan Wyrwicz
- Annika Behrendt
- Diana Born
- Sophie Dahl
- Marcel Dammert
- Sandra Diebel
- Maria Hammer
- Lisa Joedicke
- Sara Kalman
- Steffen Klein
- Daniel Krueger
- Christine Mäder
- Sabina Merrill
- Lora Nacheva
- Tobias Schmidt
- Christian Schroeter
- Angelina Staudt
- Lukas Welti
University of EdinburghSchool of Biological Sciences,
EH9 3JR Edinburgh, United Kingdom
- Andrew Chatr Aryamontri
University CollegeSchool of Medicine and Medical Science,,
4 Dublin, Ireland
- Gleb Grebnev
- Niall Haslam
University of SouthamptonCentre for Biological Sciences,
SO17 1BJ Southampton, United Kingdom
- Rich Edwards
Paul Scherrer InstitutBiomolecular Research,
CH-5232 Villigen, Switzerland
- Michel Steinmetz
91054 Erlangen-Nürnberg, Germany
- Heike Meiselbach
M. Sklodowska-Curie Cancer Center and Institute of OncologyLaboratory of Bioinformatics and Systems Biology,
WK Roentgena 5,
02-781 Warsaw, Poland
- Magda Dymecka
- Martha Kuban
Ecole supérieure de biotechnologieBld Sébastien Brandt,
67412 Illkirch, France
- Gilles Travé
Pab II, 4th floor, Lab QB-9,
Buenos Aires, Argentina
- Juliana Glavina
Our consortium has made ELM into the largest resource for functional sites in proteins. Yet there is much that we would like to do in the future to enhance the resource. In order to do so, we need new sources of funding and support. If possible, we would like to keep the ELM webserver and pipeline resources free for all users including in Industry but we do not know if we will be able to sustain this in future.
If your company finds ELM useful, you might wish to enter an industrial sponsorship with us, e.g. by funding one or more ELM developers. As well as helping to ensure that ELM is applied effectively by you in-house, ELM partners all have extensive bioinformatics knowledge and could, for example, offer more general consultancy and training to their sponsors. Furthermore, your company may influence the future path of development of the ELM resource towards functionalities that will be particularly useful for your company.
If you are interested, send direct enquiries to: Dr. Toby J. Gibson, EMBL, Heidelberg or to one of our academic partners in Bergen, Dundee, Rome or Poznan:
ELM data can be downloaded & distributed for non-commercial use according to the ELM Software License Agreement