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Podobnostní vyhledávání v databázích proteinových struktur / Similarity Search in Protein Structure Databases

Proteins are one of the most important biopolymers having a wide range of functions in living organisms. Their huge functional diversity is achieved by their ability to fold into various 3D structures. Moreover, it has been shown that proteins sharing similar structure often share also other properties (e.g, a biological function, an evolutionary origin, etc.). Therefore, protein structures and methods to identify their similarities are so widely studied. In this thesis, we introduce a system allowing similarity search in pro- tein structure databases. The system retrieves, given a query structure, all database structures being similar to the query structure. It employs several key components. We have introduced a novel similarity measure assigning similarity scores to pairs of protein structures. We have designed specific access method based on LAESA metric indexing and using the proposed measure. The access method allows to search similar structures more effi- ciently than when a sequential scan of a database is employed. To achieve further speedup, the measure and the access method have been parallelized, resulting in almost linear speedup with the respect to the number of available cores. The last component is a web user interface that allows to accept a query structure and to present a list of...

Identiferoai:union.ndltd.org:nusl.cz/oai:invenio.nusl.cz:306307
Date January 2012
CreatorsGalgonek, Jakub
ContributorsSkopal, Tomáš, Porto, Markus, Svozil, Daniel
Source SetsCzech ETDs
LanguageEnglish
Detected LanguageEnglish
Typeinfo:eu-repo/semantics/doctoralThesis
Rightsinfo:eu-repo/semantics/restrictedAccess

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