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FEBS Short-Term Fellowships
Similarity Retrieval in Protein Structure Databases
2012 - 2012

Similarity retrieval has a wide usage in many bioinformatics tasks. A typical case is similarity retrieval in databases of protein structures. However, this problem is not satisfactorily solved yet, especially in the comparison with the similarity retrieval in databases of protein sequences which is successfully solved (e.g., by BLAST).

Thus, the goal of our proposed research is to develop a tool for similarity retrieval in protein structure databases. The tool will be accessible online as a web application that will support not only protein structures but also protein sequences as a query input. In the case that a query is the sequence of a protein, the system should select such structures that are similar to the (unknown) structure of the query protein. In general, such behavior can be achieved by use of so-called sequence-structure similarity measures.

The guest laboratory (AG Porto) has extensive experiences with the design of the protein structure similarities and also with sequence-structure similarities. Our research group (SIRET) develops efficient and effective methods for similarity retrieval in huge databases. We have also experience with application of these methods on biological data. Hence, we hope that the joint research can result in a tool solving the problem with higher efficiency and effectiveness.

Principal investigator : Jakub Galgonek