PROTDNABINDSPEC

Inferring DNA binding specificities through in silico folding of natively unstructured protein regions

Coordinatore	UNIVERSITY COLLEGE LONDON    more  Organization address address: GOWER STREET city: LONDON postcode: WC1E 6BT contact info Titolo: Ms. Nome: Greta Cognome: Borg- Carbott Email: send email Telefono: 442031000000 Fax: 442031000000
Nazionalità Coordinatore	United Kingdom [UK]
Totale costo	0 €
EC contributo	163˙702 €
Programma	FP7-PEOPLE Specific programme "People" implementing the Seventh Framework Programme of the European Community for research, technological development and demonstration activities (2007 to 2013)
Code Call	FP7-PEOPLE-IEF-2008
Funding Scheme	MC-IEF
Anno di inizio	2009
Periodo (anno-mese-giorno)	2009-09-04   -   2011-09-03

 Partecipanti

#	participant	country	role	EC contrib. [€]
1	UNIVERSITY COLLEGE LONDON  Organization address address: GOWER STREET city: LONDON postcode: WC1E 6BT contact info Titolo: Ms. Nome: Greta Cognome: Borg- Carbott Email: send email Telefono: 442031000000 Fax: 442031000000	UK (LONDON)	coordinator	163˙702.69

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 Obiettivo del progetto (Objective)

'A major challenge in post genome biology is the functional assignment of gene products. An important goal is the identification and characterization of DNA binding proteins – especially transcription factors – and of their specific target sequences. Recent strategies for determining protein-DNA binding specificities combine experimental high throughput data with bioinformatics algorithms providing encouraging results. Structure based approaches are particularly promising, as they can predict previously undetected binding sites and open the road to the rational design of novel regulatory molecules. This project aims at expanding our current knowledge of protein-DNA binding modes. We will use structural bioinformatics methods for predicting the structure and specificity of DNA binding proteins, focusing in particular on natively unfolded protein regions (flexible segments that do not assume a fixed conformation in the native state, but become ordered upon binding) which are frequently observed in DNA binding proteins. We will first develop a general method for predicting the atomic coordinates of the DNA bound conformation of these proteins combining fragment based methods for protein structure prediction and novel DNA-protein specific energy potentials. Predicted complexes will be subsequently used to predict DNA binding sites in genomes and the accuracy assessed on the basis of available experimental reference data. The results of this project will improve our understanding of the molecular details of protein-DNA interactions, assist the annotation of genomes, and prioritize experiments aimed at verifying the predicted specificities. On a more general level, this research will further advance knowledge in the field of macromolecular interactions, a central problem in systems biology.'