Acknowledgements
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.
- CellZome
- Become an ELM sponsor?
The ELM logo was designed by:
- Petra Riedinger, Graphic Designer, Office of Information and Public Affairs, EMBL.
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:
- These web-pages are delivered by Apache HTTP Server
and the python web framework
- Most programming is done with the object-oriented language Python.
- The ELM database is powered by the object relational database management system PostgreSQL
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.
References:
ELM (while citing ELM please also cite our most recent paper):
-
ELM—the eukaryotic linear motif resource in 2020.
Kumar M, Gouw M, Michael S, Sámano-Sánchez H, Pancsa R, Glavina J, Diakogianni A, Valverde JA, Bukirova D, Čalyševa J, Palopoli N, Davey NE, Chemes LB, Gibson TJ. (2020) Nucleic Acids Res., Jan, 2020 -
The eukaryotic linear motif resource - 2018 update.
Gouw M, Michael S, Sámano-Sánchez H, Kumar M, Zeke A, Lang B, Bely B, Chemes LB, Davey NE, Deng Z, Diella F, Gürth CM, Huber AK, Kleinsorg S, Schlegel LS, Palopoli N, Roey KV, Altenberg B, Reményi A, Dinkel H, Gibson TJ. (2018) Nucleic Acids Res., Jan, 2018 -
ELM 2016 -- data update and new functionality of the eukaryotic linear motif resource
Dinkel H, Van Roey K, Michael S, Kumar M, Uyar B, Altenberg B, Milchevskaya V, Schneider M, Kühn H, Damerell V, Diebel S, Kalman S, Klein S, Knudsen AC, Mäder C, Merrill S, Staudt A, Thiel V, Welti L, Davey NE, Diella F, Gibson TJ. (2016) Nucleic Acids Res., Nov, 2015 -
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
Further Reading:
-
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:
EMBL Heidelberg
Biocomputing Unit,Meyerhofstrasse 1,
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
- Jesus Alvarado Valverde
- Peer Bork
- Nigel Brown
- Aidan Budd
- Dayana Bukirova
- Jelena Čalyševa
- Sophie Chabanis-Davidson
- Claudia Chica
- Victoria Damerell
- Norman Davey
- Ziqi Deng
- Athina Diakogianni
- Francesca Diella
- Holger Dinkel
- Laszlo Dobson
- Christine Gemünd
- Toby Gibson
- Kate Gould
- Rambabu Gudavalli
- Peter Jehl
- Arne Knudsen
- Helen Kühn
- Manjeet Kumar
- Ivica Letunic
- Rune Linding
- Katja Luck
- Caroline McGuigan
- Balint Meszaros
- Sushama Michael
- Vladislava Milchevskaya
- Chenna Ramu
- Hugo Sámano-Sánchez
- Davide Sampietro
- Markus Seiler
- Tobias Speck
- Vera Thiel
- Grischa Toedt
- Bora Uyar
- Kim van Roey
- Robert Weatheritt
University of Rome - Tor Vergata
Center for Molecular Bioinformatics,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
University of Bergen, HIB
Department of Molecular Biology,Thormoelensgt. 55,
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
University of Dundee
Department of Biochemistry,WTB/MSI complex,
DD1 5EH Dundee, Scotland UK
The School of Life Sciences at Dundee is a centre for research into biological phosphorylation. The ELM partner is Bill Hunter who applies X-ray crystallography to the study of enzymatic processes.
- Scott Cameron
- William Hunter
- David Martin
CellZome GmbH
Meyerhofstrasse 1,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
BioInfoBank Institute
Biocomputing,Limanowskiego 24A/16,
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
Heidelberg University
69117 Heidelberg, Germany- Annika Behrendt
- Diana Born
- Sophie Dahl
- Marcel Dammert
- Sandra Diebel
- Clara-Marie Guerth
- Maria Hammer
- Ann-Kathrin Huber
- Lisa Joedicke
- Melanie Kaeser
- Sara Kalman
- Steffen Klein
- Stefan Kleinsorg
- Daniel Krueger
- Christine Mäder
- Sabina Merrill
- Lora Nacheva
- Lara Sophie Schlegel
- Tobias Schmidt
- Christian Schroeter
- Angelina Staudt
- Lukas Welti
University of Edinburgh
School of Biological Sciences,Mayfield Road,
EH9 3JR Edinburgh, United Kingdom
- Andrew Chatr Aryamontri
University College
School of Medicine and Medical Science,,Belfield,
4 Dublin, Ireland
- Gleb Grebnev
- Niall Haslam
University of Southampton
Centre for Biological Sciences,Highfield Campus,
SO17 1BJ Southampton, United Kingdom
- Rich Edwards
Paul Scherrer Institut
Biomolecular Research,PSI,
CH-5232 Villigen, Switzerland
- Michel Steinmetz
Friedrich-Alexander-Universität
Bioinformatik,Fahrstraße 17,
91054 Erlangen-Nürnberg, Germany
- Heike Meiselbach
M. Sklodowska-Curie Cancer Center and Institute of Oncology
Laboratory of Bioinformatics and Systems Biology,WK Roentgena 5,
02-781 Warsaw, Poland
- Magda Dymecka
- Martha Kuban
Ecole supérieure de biotechnologie
Bld Sébastien Brandt,67412 Illkirch, France
- Gilles Travé
Universidad de Buenos Aires
Departamento de Química Biológica,Pab II, 4th floor, Lab QB-9,
Buenos Aires, Argentina
- Juliana Glavina
Institute of Enzymology
,,
Budapest, Hungary
- Rita Pancsa
- András Zeke
Leloir Institute
,,
Buenos Aires, Argentina
- Lucia Chemes
University of Quilmes
,,
Quilmes, Argentina
- Juan Griffin
- Juan Mac Donagh
- Nicolas Palopoli
ICR
,,
London, UK
- Izabella Krystkowiak
- Mihkel Ord
VUB
,,
Brussels, Belgium
- Nazanin Farahi
- Tamas Lazar
Justus Liebig University Giessen
,,
Giessen, Germany
- Ramya Kraleti
Birla Institute of Technology & Science
,Vidya Vihar,
Rajasthan 333031 Pilani, India
- Anurag Nagpal
Eotvos Lorand University
,,
Budapest, Hungary
- Zsofia Dobson-Kalman
University College Cork
,,
Cork, Ireland
- Kellie Dean
Pázmány Péter Catholic University
,,
Budapest, Hungary
- Eszter Kanta
Japan
,,
Japan, Japan
- Stefano Pascarelli
UNSAM
,,
BUENOS AIRES, ARGENTINA
- Carmen Florencia Suarez
Is your Company interested in sponsoring ELM?
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:
Bergen partner: Dr. Rein Aasland
Dundee partner: Dr. Bill Hunter
Rome partner: Dr. Manuela Helmer Citterich
Poznan partner: Dr. Leszek Rychlewski
ELM data can be downloaded & distributed for non-commercial use according to the ELM Software License Agreement