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rdf:type
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Description
| - There is a paramount need to develop new techniques and tools that will extract as much information as possible from the ever growing repository of protein 3D structures. We report here on the development of a software tool for the multiple superimposition of large sets of protein structural motifs. Our superimposition methodology performs a systematic search for the atom pairing that provides the best fit. During this search, the RMSD values for all chemically relevant pairings are calculated by quaternion algebra. The number of evaluated pairings is markedly decreased by using PDB annotations for atoms. This approach guarantees that the best fit will be found and can be applied even when sequence similarity is low or does not exist at all. We have implemented this methodology in the Web application SiteBinder, which is able to process up to thousands of protein structural motifs in a very short time, and which provides an intuitive and user-friendly interface.
- There is a paramount need to develop new techniques and tools that will extract as much information as possible from the ever growing repository of protein 3D structures. We report here on the development of a software tool for the multiple superimposition of large sets of protein structural motifs. Our superimposition methodology performs a systematic search for the atom pairing that provides the best fit. During this search, the RMSD values for all chemically relevant pairings are calculated by quaternion algebra. The number of evaluated pairings is markedly decreased by using PDB annotations for atoms. This approach guarantees that the best fit will be found and can be applied even when sequence similarity is low or does not exist at all. We have implemented this methodology in the Web application SiteBinder, which is able to process up to thousands of protein structural motifs in a very short time, and which provides an intuitive and user-friendly interface. (en)
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Title
| - SiteBinder: An improved approach for comparing multiple protein structural motifs
- SiteBinder: An improved approach for comparing multiple protein structural motifs (en)
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skos:prefLabel
| - SiteBinder: An improved approach for comparing multiple protein structural motifs
- SiteBinder: An improved approach for comparing multiple protein structural motifs (en)
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skos:notation
| - RIV/00216224:14310/12:00057316!RIV13-GA0-14310___
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http://linked.open...avai/riv/aktivita
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http://linked.open...avai/riv/aktivity
| - P(GD301/09/H004), P(ME08008)
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http://linked.open...iv/cisloPeriodika
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http://linked.open...vai/riv/dodaniDat
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http://linked.open...aciTvurceVysledku
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http://linked.open.../riv/druhVysledku
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http://linked.open...iv/duvernostUdaju
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http://linked.open...titaPredkladatele
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http://linked.open...dnocenehoVysledku
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http://linked.open...ai/riv/idVysledku
| - RIV/00216224:14310/12:00057316
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http://linked.open...riv/jazykVysledku
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http://linked.open.../riv/klicovaSlova
| - protein structural motifs; superimposition; comparison; lectins; apoptosis (en)
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http://linked.open.../riv/klicoveSlovo
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http://linked.open...odStatuVydavatele
| - US - Spojené státy americké
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http://linked.open...ontrolniKodProRIV
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http://linked.open...i/riv/nazevZdroje
| - Journal of Chemical Information and Modeling
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http://linked.open...in/vavai/riv/obor
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http://linked.open...ichTvurcuVysledku
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http://linked.open...cetTvurcuVysledku
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http://linked.open...vavai/riv/projekt
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http://linked.open...UplatneniVysledku
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http://linked.open...v/svazekPeriodika
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http://linked.open...iv/tvurceVysledku
| - Koča, Jaroslav
- Wimmerová, Michaela
- Geidl, Stanislav
- Huber, Heinrich J.
- Ionescu, Crina-Maria
- Sehnal, David
- Svobodová Vařeková, Radka
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http://linked.open...ain/vavai/riv/wos
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issn
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number of pages
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http://bibframe.org/vocab/doi
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http://localhost/t...ganizacniJednotka
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