About: P3S: Protein Structure Similarity Search     Goto   Sponge   NotDistinct   Permalink

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Description
  • Similarity search in protein structure databases is an important task of computational biology. To reduce the time required to search for similar structures, indexing techniques are being often introduced. However, as the indexing phase is computationally very expensive, it becomes useful only when a large number of searches are expected (so that the expensive indexing cost is amortized by cheaper search cost). This is a typical situation for a public similarity search service. In this article we introduce the P3S web application (http://siret.cz/p3s) allowing, given a query structure, to identify the set of the most similar structures in a database. The result set can be browsed interactively, including visual inspection of the structure superposition, or it can be downloaded as a zip archive. P3S employs the SProt similarity measure and an indexing technique based on the LAESA method, both introduced recently by our group. Together with the measure and the index, the method presents an effective and efficient tool for querying protein structure databases.
  • Similarity search in protein structure databases is an important task of computational biology. To reduce the time required to search for similar structures, indexing techniques are being often introduced. However, as the indexing phase is computationally very expensive, it becomes useful only when a large number of searches are expected (so that the expensive indexing cost is amortized by cheaper search cost). This is a typical situation for a public similarity search service. In this article we introduce the P3S web application (http://siret.cz/p3s) allowing, given a query structure, to identify the set of the most similar structures in a database. The result set can be browsed interactively, including visual inspection of the structure superposition, or it can be downloaded as a zip archive. P3S employs the SProt similarity measure and an indexing technique based on the LAESA method, both introduced recently by our group. Together with the measure and the index, the method presents an effective and efficient tool for querying protein structure databases. (en)
Title
  • P3S: Protein Structure Similarity Search
  • P3S: Protein Structure Similarity Search (en)
skos:prefLabel
  • P3S: Protein Structure Similarity Search
  • P3S: Protein Structure Similarity Search (en)
skos:notation
  • RIV/00216208:11320/13:10124114!RIV14-GA0-11320___
http://linked.open...avai/riv/aktivita
http://linked.open...avai/riv/aktivity
  • P(GAP202/11/0968), S
http://linked.open...vai/riv/dodaniDat
http://linked.open...aciTvurceVysledku
http://linked.open.../riv/druhVysledku
http://linked.open...iv/duvernostUdaju
http://linked.open...titaPredkladatele
http://linked.open...dnocenehoVysledku
  • 101110
http://linked.open...ai/riv/idVysledku
  • RIV/00216208:11320/13:10124114
http://linked.open...riv/jazykVysledku
http://linked.open.../riv/klicovaSlova
  • web service; similarity retrieval; protein structure (en)
http://linked.open.../riv/klicoveSlovo
http://linked.open...ontrolniKodProRIV
  • [C94BC6C08A67]
http://linked.open...v/mistoKonaniAkce
  • Rhodes Islands, Greece
http://linked.open...i/riv/mistoVydani
  • Neuveden
http://linked.open...i/riv/nazevZdroje
  • Euro-Par 2012: Parallel Processing Workshops
http://linked.open...in/vavai/riv/obor
http://linked.open...ichTvurcuVysledku
http://linked.open...cetTvurcuVysledku
http://linked.open...vavai/riv/projekt
http://linked.open...UplatneniVysledku
http://linked.open...iv/tvurceVysledku
  • Skopal, Tomáš
  • Hoksza, David
  • Galgonek, Jakub
http://linked.open...vavai/riv/typAkce
http://linked.open.../riv/zahajeniAkce
issn
  • 0302-9743
number of pages
http://bibframe.org/vocab/doi
  • 10.1007/978-3-642-36949-0_26
http://purl.org/ne...btex#hasPublisher
  • Springer-Verlag. (Berlin; Heidelberg)
https://schema.org/isbn
  • 978-3-642-36948-3
http://localhost/t...ganizacniJednotka
  • 11320
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