Objective
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.
Fields of science (EuroSciVoc)
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques. See: The European Science Vocabulary.
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques. See: The European Science Vocabulary.
- natural sciences biological sciences genetics
- natural sciences computer and information sciences databases
- natural sciences biological sciences biochemistry biomolecules proteins
- natural sciences biological sciences molecular biology structural biology
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Keywords
Project’s keywords as indicated by the project coordinator. Not to be confused with the EuroSciVoc taxonomy (Fields of science)
Project’s keywords as indicated by the project coordinator. Not to be confused with the EuroSciVoc taxonomy (Fields of science)
Programme(s)
Multi-annual funding programmes that define the EU’s priorities for research and innovation.
Multi-annual funding programmes that define the EU’s priorities for research and innovation.
Topic(s)
Calls for proposals are divided into topics. A topic defines a specific subject or area for which applicants can submit proposals. The description of a topic comprises its specific scope and the expected impact of the funded project.
Calls for proposals are divided into topics. A topic defines a specific subject or area for which applicants can submit proposals. The description of a topic comprises its specific scope and the expected impact of the funded project.
Call for proposal
Procedure for inviting applicants to submit project proposals, with the aim of receiving EU funding.
Procedure for inviting applicants to submit project proposals, with the aim of receiving EU funding.
FP7-PEOPLE-2007-4-3-IRG
See other projects for this call
Funding Scheme
Funding scheme (or “Type of Action”) inside a programme with common features. It specifies: the scope of what is funded; the reimbursement rate; specific evaluation criteria to qualify for funding; and the use of simplified forms of costs like lump sums.
Funding scheme (or “Type of Action”) inside a programme with common features. It specifies: the scope of what is funded; the reimbursement rate; specific evaluation criteria to qualify for funding; and the use of simplified forms of costs like lump sums.
Coordinator
31905 Haifa
Israel
The total costs incurred by this organisation to participate in the project, including direct and indirect costs. This amount is a subset of the overall project budget.