SAS'txt mining

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SAS.txt mining the ELM Resource Rune Linding
ELM Consortium Gibson Team EMBL Biocomputing
Unit
http//elm.eu.org The Eukaryotic Linear motif
resource
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Src a modular protein
CSK phosphorylation (Y527) SH2 ligand
Myristoylation site
SH3 ligand
Auto phosphorylation site (Y416)
60-80 of all proteins are multidomain/modular
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Functional Site Classes
Functional Group
Functional Sites (ELMs)
Size
Targeting signals
KDEL, NLS, NES Mitochondrial Import
signals PTSI/II, Signal peptides
30 150 150 2 30
Linear protein interaction sites
EH,PDZ,SH2,SH3,WW,PCNA,LLXXL Calmodulin/Cyclin
binding ?-helix Protease inhibitors Active
peptides and hormones
Covalent modification sites
Phosphorylation, methylation, acetylation glycosyl
ation, fucosylation prenylation, myristoylation,
ubiquitinylation
RNA interaction motifs
RX,RGY motifs
Processing Sites
Diverse protease cleavage targets in secretion,
apoptosis etc.
lt 400 Functional sites 5k ELMs gt100k
Instances/proteome
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ELM projectEU consortium

• Question
• What short motifs are in my protein?
• Answer
• Can't say using current bioinformatics resources!
• ELM consortium targets
• provide annotated database of functional
  sites/ELMs - siteseeing
• provide software for prediction of ELMs
• investigate predictions experimentally

EMBL-HD - Uni Roma II - Uni Dundee WTC
Bioinfo.pl - CellZome GmbH Uni Bergen
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SH3 ligands
LIG_SH3_1
LIG_SH3_2
P..P.RK
RKY..P..P
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Beyond sequence analysis...

• Sequence analysis brought Bioinformatics to the
  center of modern bioscience
• ...but it can't solve the ELM problem...overpredic
  tion!
• The ELM Resource try to solve the problem using
  knowledge and rule-based (AI) technology....
• We call it contextual filtering or knowledge
  based decision support (KBDS)

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KBD supporters
72-77 (acc. 98)
147-152 (acc. 81)
HIV Nef protein
SH3 domain
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ELM information flow
Literature
KBDS extraction
Protein space - sequence space
(SWALL,SMART...) - structure space (PDB) - fold
space (SCOP)
Unpublished data
Reading! 100 papers/ELM Tourist-office Siteseers
(ELM annotators)

• DataCollectors(scripts.py)
• ELM resource
• Siteseers
• Geeks/Coders

ELMIO
SQL RDBMS
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More on ELM...
http//elm.eu.org NAR 2003 web issue(this
week) ISMB2003 Poster D2 BOSC2003 Talk
tomorrow at 9? ELM demo tuesday afternoon