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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:
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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
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Cell regulation: determined to signal discrete cooperation
Gibson, T.J. (2009). Trends Biochem Sci., 34(10): 471-82
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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.
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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
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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.
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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.
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The ELM Consortium |
The ELM consortium involves
five European academic institutions and
one biotechnology company, and was funded
by EU. |
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University
of 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. Full
time ELMer:
- Pål
Puntervoll - siteseeing,
software development,
webmaster
- Morten Mattingsdal - siteseeing
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BioInfo.PL
(Poland)
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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. ELMers at
BioInfo.PL:
- Leszek
Rychlewski - ab
initio filter
- Krzysztof Ginalski - ab initio
filter
- Andrzej Kierzek - system
development
- Jakub Pas - structural
filters
- Lucjan Wyrwicz - siteseeing
- Marcin von Grotthuss -
structural filters
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University
of Dundee (Scotland) |
| 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. Full time ELMer:
- Scott Cameron - siteseeing
- David Martin - consultant
(part time)
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CellZome
(Germany)
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| CellZome
is a functional genomics
company. Giulio Superti-Furga
is the ELM partner whose
research interests are
in tyrosine phosphoylation.
ELMers at CellZome:
- Francesca
Diella - siteseeing
- Bernhard Kuster - mass spectrometry
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Acknowledgements |
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The ELM
project is/
was funded
by: |
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We use
SMART for filtering |
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- Thanks to Ivica Letunic
for the script.
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The ELM
logo was designed by: |
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EU.org |
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- We are very grateful
to the people at EU.org
for providing the elm.eu.org
domain for free.
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The ELM
project is powered by: |
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- Most programming is
done with the object-oriented
language Python.
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- The ELM database is
powered by the object
relational database
management system PostgreSQL.
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Is your Company interested in sponsoring ELM?
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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 |
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| Last
modified 02-FEB-2010 - webmaster |
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