About: SiteBinder: An improved approach for comparing multiple protein structural motifs

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An Entity of Type : http://linked.opendata.cz/ontology/domain/vavai/Vysledek, within Data Space : linked.opendata.cz associated with source document(s)

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
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)
Title	SiteBinder: An improved approach for comparing multiple protein structural motifs SiteBinder: An improved approach for comparing multiple protein structural motifs (en)
skos:prefLabel	SiteBinder: An improved approach for comparing multiple protein structural motifs SiteBinder: An improved approach for comparing multiple protein structural motifs (en)
skos:notation	RIV/00216224:14310/12:00057316!RIV13-GA0-14310___
http://linked.open...avai/riv/aktivita	P
http://linked.open...avai/riv/aktivity	P(GD301/09/H004), P(ME08008)
http://linked.open...iv/cisloPeriodika	2
http://linked.open...vai/riv/dodaniDat	2013
http://linked.open...aciTvurceVysledku	Koča, Jaroslav Wimmerová, Michaela Sehnal, David Geidl, Stanislav Svobodová Vařeková, Radka Ionescu, Crina-Maria
http://linked.open.../riv/druhVysledku	J - Článek v odborném periodiku
http://linked.open...iv/duvernostUdaju	S - Úplné a pravdivé údaje nepodléhající ochraně podle zvláštních právních předpisů
http://linked.open...titaPredkladatele	Masarykova univerzita / Přírodovědecká fakulta
http://linked.open...dnocenehoVysledku	168181
http://linked.open...ai/riv/idVysledku	RIV/00216224:14310/12:00057316
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	protein structural motifs; superimposition; comparison; lectins; apoptosis (en)
http://linked.open.../riv/klicoveSlovo	lectins comparison protein structural motifs superimposition apoptosis
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[C63E73755505]
http://linked.open...i/riv/nazevZdroje	Journal of Chemical Information and Modeling
http://linked.open...in/vavai/riv/obor	CF
http://linked.open...ichTvurcuVysledku	6 (xsd:int)
http://linked.open...cetTvurcuVysledku	7 (xsd:int)
http://linked.open...vavai/riv/projekt	Molecular and structural biology of selected antitumor drugs. From mechanistic studies to chemotherapy of tumors Design of Carbohydrates and Glycomimetics as Antibacterial and Antiviral Drugs
http://linked.open...UplatneniVysledku	2012
http://linked.open...v/svazekPeriodika	52
http://linked.open...iv/tvurceVysledku	Koča, Jaroslav Wimmerová, Michaela Geidl, Stanislav Huber, Heinrich J. Ionescu, Crina-Maria Sehnal, David Svobodová Vařeková, Radka
http://linked.open...ain/vavai/riv/wos	000300650400009
issn	1549-9596
number of pages	17 (xsd:int)
http://bibframe.org/vocab/doi	10.1021/ci200444d
http://localhost/t...ganizacniJednotka	14310

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