Objectif Finding the structural neighbors of a protein is an essential task in computational structural Biology. In cases where there is no detectable sequence similarity, the identification of structural neighbors offers a powerful approach to predicting structure and function. State-of-the-art protein structural searches find structural neighbors by comparing a protein to all proteins in their database. As this is an expensive computation that depends directly on the size of the database, such searches consider only a representative subset of the Protein Data Bank (PDB). The PDB is growing dramatically to include many structures of uncharacterized function solved by high-throughput methods developed by the Structural Genomics (SG) initiative. Characterizing these structures, and addressing questions raised by the improved coverage of structure space, mandates better structure search tools. I propose to develop a search tool for protein structure space that is analogous to web search tools such as Google. The system is designed to be fast and interactive, to cover the whole data set, and to have a clear and simple interface so that it can serve as a navigation interface to structure space. For this, I propose adapting a data structure called an inverted index, which is used for fast retrieval in web search. Protein structures are described as strings of letter strings based on a structural alphabet, and placed in an inverted index. Then, given a query structure and its string description, one can quickly retrieve a short list of candidate structural neighbors. Similar to web search, I suggest using query expansion to improve the retrieval performance. The proposal also includes an application of structural search for comparing the structural novelty of contributions from different SG centers. This project will enable me to establish a new Computational Biology research team at my host institution: it preeminently fulfills the goals of the Work Program. Champ scientifique natural sciencesbiological sciencesgeneticsnatural sciencescomputer and information sciencesdatabasesnatural sciencesbiological sciencesbiochemistrybiomoleculesproteinsnatural sciencesbiological sciencesmolecular biologystructural biology Mots‑clés evaluation of structural novelty of SG proteins inverted index for protein structures protein structural alphabets application query expansion for protein structure search engine for PDB Programme(s) FP7-PEOPLE - Specific programme "People" implementing the Seventh Framework Programme of the European Community for research, technological development and demonstration activities (2007 to 2013) Thème(s) PEOPLE-2007-4-3.IRG - Marie Curie Action: "International Reintegration Grants" Appel à propositions FP7-PEOPLE-2007-4-3-IRG Voir d’autres projets de cet appel Régime de financement MC-IRG - International Re-integration Grants (IRG) Coordinateur UNIVERSITY OF HAIFA Contribution de l’UE € 100 000,00 Adresse ABBA KHUSHY BLVD MOUNT CARMEL 31905 Haifa Israël Voir sur la carte Type d’activité Higher or Secondary Education Establishments Contact administratif Suzan Aminpour (Ms.) Liens Contacter l’organisation Opens in new window Site web Opens in new window Coût total Aucune donnée