The Eukaryote Linear Motif resource for Functional Sites in Proteins

Acknowledgements

The ELM project is/was funded by:

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:

  • These web-pages are delivered by Apache HTTP Server

    and the python web framework DJANGO
  • 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 eukarytic 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:

External tools used:

Further Reading:

o The ELM Consortium

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
  • Peer Bork
  • Nigel Brown
  • Aidan Budd
  • Sophie Chabanis-Davidson
  • Claudia Chica
  • Norman Davey
  • Francesca Diella
  • Holger Dinkel
  • Christine Gemünd
  • Toby Gibson
  • Kate Gould
  • Rambabu Gudavalli
  • Peter Jehl
  • Helen Kühn
  • Ivica Letunic
  • Rune Linding
  • Katja Luck
  • Caroline McGuigan
  • Sushama Michael
  • Chenna Ramu
  • Kim Roey, van
  • Markus Seiler
  • Tobias Speck
  • Grischa Toedt
  • Bora Uyar
  • 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
  • Diana Born
  • Marcel Dammert
  • Sandra Diebel
  • Maria Hammer
  • Lisa Joedicke
  • Daniel Krueger
  • Christine Mäder
  • Sabina Merrill
  • Tobias Schmidt
  • Christian Schroeter
  • 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

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

Please cite: The Eukaryotic Linear Motif Resource ELM: 10 Years and Counting (PMID:24214962)

ELM data can be downloaded and distributed for non-commercial use according to the ELM Software License Agreement
feedback@elm.eu.org