GeneFun - Deliverables

GeneFun

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Deliverable by GeneFun

Deliverable No^¹	Deliverable title	Delivery date ^²	Nature ^³	Dissemination level ^⁴	Group responsible
D1.1	Clustering tools for automatically generating protein families and subfamilies that reproduce groups of proteins with consistent and meaningful functional annotations	6	R	PP	ULB
D1.2	A first set of protein families and subfamilies to be used in other workpackages	6	R	PP	ULB
D1.3	Methods for organising sequence space on the basis of multiple structure alignments	12	D	PU	ULB
D1.4	An improved set of protein families and subfamilies derived using clustering procedures	18	R	PP	ULB
D1.5	A comprehensive set of protein families and subfamilies derived using multiple structure alignments	24	R	PU	ULB
D2.1	Reliability score for function transfer based on pairwise similarities	6	R	PP	CNB
D2.2	Reliability score for function transfer based family-level similarities	12	R	PP	CNB
D2.3	Stand alone tool for evaluating function transfer reliability in genome annotation procedures	24	D	PU	CNB
D2.4	reliability estimation tools as plug-ins other sequence analysis tools and systems	36	D	PU	CNB
D3.1	Methods for the reliable delineation of domain architecture (DA)	6	R	PP	SBC
D3.2	Methods for prediction of functional features from DA	12	R	PP	SBC
D3.3	Results on benchmarks of methods for predicting interactions from DA	18	R	PP	SBC
D3.4	Improved methods for prediction of function and interactions from DA from a larger set of proteins with reliable annotations	24	D	PU	SBC
D3.5	Function prediction from DA for non annotated protein regions	36	R	PU	SBC
D4.1	framework for data representation and management	2	R	PP	BIB
D4.2	protein structure modelling engine coupled to the function prediction system	4	R	PP	BIB
D4.3	database of enzyme structures coupled to the function prediction system	6	R	PP	BIB
D4.4	linear and no-linear functional signatures coupled to the function prediction system	20	D	PU	BIB
D4.5	identification of functional site by stability measures for enzymes	6	P	PP	BIB
D4.6	identification of interfaces of obligate (high affinity) complexes	12	P	PP	BIB
D4.7	identification of interaction partners for Zinc-finger domains	8	R	PU	BIB
D4.8	identification of interaction partners for other types of peptide-binding modules	36	R	PU	BIB
D4.9	tailored structure based function prediction prototype for 5 fold families	24	R	PU	BIB
D4.10	Prediction of the effects of SNPs	36	R	PU	BIB
D5.1	A WEB server architecture that is able to incorporate the heterogeneous interaction prediction methods	12	P	PP	EMBL2
D5.2	Implementation of at least four distinct computational methods and of experimental data (gene expression, complex purification, yeast 2 hybrid sets)	24	R	PP	EMBL2
D5.3	A set of interactions and relationships between genes and proteins extracted from the literature	24	R	PP	EMBL2
D5.4	Large-scale novel function assignments for all annotated $B!H(Bhypothetical$B!I(B genes in all sequenced genomes	36	R	PU	EMBL2
D5.5	Training courses on the features of this complex function prediction tool	24	D	PU	EMBL2
D6.1	First version of the Integrated Meta-server, with a first set of protocols for combining homology, and context based methods	18	D	PP	EMBL2/CNB
D6.2	Prototype version of the Integrated Meta-server	24	R	PU	EMBL2/CNB
D6.3	Training courses on the features of this integreated function prediction tool	24	D	PU	EMBL2/CNB
D6.4	Improved function assignment for eukaryotic generes using the server	24-36	R	PU	EMBL2/CNB
D7.1	Six additional new assays for protein characterisation	12	D	PP	OCI
D7.2	Cloning expression and purification of 100 target proteins	24	D	PP	OCI
D7.3	Structural and functional characterisation of soluble proteins	36	R	PP	OCI

Footnotes

1Deliverable numbers in order of delivery dates:

2Month in which the deliverables will be available. Month 0 marking the start of the project, and all delivery dates being relative to this start date.

3Please indicate the nature of the deliverable using one of the following codes:

R = Report

P = Prototype

D = Demonstrator

O = Other

4Please indicate the dissemination level using one of the following codes:

PU = Public

PP = Restricted to other programme participants (including the Commission Services)

RE = Restricted to a group specified by the consortium (including the Commission Services)

CO = Confidential, only for members of the consortium (including the Commission Services)

Arne Elofsson

Last modified: Sat Apr 30 14:19:13 CEST 2005