Deliverables and Workpackages
|
1 |
Protein families and subfamilies (DF) |
Delivery |
1-6 |
7 12 |
13-18 |
19-24 |
25-30 |
31-36 |
Nature |
Dissemination |
Status |
|
1.1 |
Clustering tools |
6 |
SW |
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R |
PP |
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1.2 |
A first set of protein families |
6 |
SW |
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R |
PP |
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1.3 |
Methods for organising sequence space |
12 |
|
AV |
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D |
PU |
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1.4 |
An improved set of protein families |
18 |
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R |
PP |
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1.5 |
A comprehensive set of protein families |
24 |
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R |
PU |
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2 |
Reliability scores for functional annotations (SW) |
Delivery |
1-6 |
7-12 |
13-18 |
19-24 |
25-30 |
31-36 |
R |
PP |
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|
2.1 |
Reliability score based on pairwise similarities |
6 |
AV |
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R |
PP |
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2.2 |
Reliability score based on family-level similarities |
12 |
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D |
PU |
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2.3 |
Stand alone tool for evaluating function transfer |
24 |
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D |
PU |
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2.4 |
reliability estimation tools as ‘plug-ins’ |
36 |
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R |
PP |
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3 |
Functional annotations from domain architecture (AE) |
Delivery |
1-6 |
7-12 |
13-18 |
19-24 |
25-30 |
31-36 |
R |
PP |
|
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3.1 |
Domain architecture (DA) for a first set of proteins |
6 |
AE |
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R |
PP |
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3.2 |
Methods for prediction of functional features from DA |
12 |
|
? |
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D |
PU |
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3.3 |
benchmarks of methods for predicting interactions from DA |
18 |
|
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R |
PU |
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3.4 |
Improved methods for prediction of function &interactions from DA |
24 |
|
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R |
PP |
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3.5 |
Function prediction from DA for non annotated protein regions |
36 |
|
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R |
PP |
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4 |
Structure-based prediction of function and interactions (LR) |
Delivery |
1-6 |
7-12 |
13-18 |
19-24 |
25-30 |
31-36 |
R |
PP |
|
|
4.1 |
framework for data representation and management |
2 |
LR |
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D |
PU |
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4.2 |
protein structure modelling engine coupled |
4 |
LR |
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P |
PP |
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4.3 |
database of enzyme structures coupled |
6 |
LR |
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P |
PP |
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4.4 |
linear and no-linear functional signatures coupled |
20 |
|
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R |
PU |
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4.5 |
identification of functional site by stability measures for enzymes |
6 |
SW |
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R |
PU |
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4.6 |
identification of interfaces of obligate (high affinity) complexes |
12 |
|
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R |
PU |
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4.7 |
identification of interaction partners for SH3 domains |
8 |
|
LR |
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R |
PU |
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4.8 |
identification of interaction partners for other modules |
36 |
|
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P |
PP |
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4.9 |
tailored structure based function prediction prototype |
24 |
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R |
PP |
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4.10 |
Prediction of the effects of SNp’s |
36 |
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R |
PP |
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5 |
Meta-server, Context-based function prediction (PB) |
Delivery |
1-6 |
7-12 |
13-18 |
19-24 |
25-30 |
31-36 |
R |
PU |
|
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5.1 |
A WEB server architecture |
12 |
|
PB |
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D |
PU |
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5.2 |
four distinct computational methods and experimental data |
24 |
|
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D |
PP |
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5.3 |
interactions and relationships extracted from the literature |
24 |
|
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R |
PU |
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5.4 |
Large-scale novel function assignments |
36 |
|
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D |
PU |
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5.5 |
Training courses |
24 |
|
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R |
PU |
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6 |
Meta-server, Integrated function prediction (PB+AV) |
Delivery |
1-6 |
7-12 |
13-18 |
19-24 |
25-30 |
31-36 |
D |
PP |
|
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6.1 |
First version of the Integrated Meta-server |
18 |
|
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D |
PP |
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6.2 |
Prototype version of the Integrated Meta-server |
24 |
|
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R |
PP |
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6.3 |
Training courses on integrated function prediction tool |
24 |
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6.4 |
Improved function assignment for eukaryotic genes using the server |
36 |
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7 |
Experimental validation of function predictions (CA) |
Delivery |
1-6 |
7-12 |
13-18 |
19-24 |
25-30 |
31-36 |
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7.1 |
Six additional new assays for protein characterisation |
12 |
|
CA |
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7.2 |
Cloning expression and purification of 100 target proteins |
24 |
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7.3 |
Structural and functional characterisation of soluble proteins |
36 |
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