About: SProt: sphere-based protein structure similarity algorithm

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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
rdfs:seeAlso	http://www.proteomesci.com/content/9/S1/S20
Description	In this paper, we proposed SProt - a novel algorithm for measuring protein structure similarity that puts emphasis on high-quality modeling of local similarities of the amino acids. This is achieved by representing each amino acid by its spatial neighborhood containing close amino acids. The approach leads to good realworld results, especially for superfamily/fold classification accuracy and for precision at high recall levels where we outperform all the compared solutions. The focus on the quality of the modeling results in high computational demands of the method. We resolve this handicap be introduction of SProt access method - a modification of LAESA metric access method - that highly decreases the runtime needed for scanning large datasets of protein structures. The speedup makes SProt competitive with the best contemporary solutions not only concerning the effectiveness but also the efficiency. In this paper, we proposed SProt - a novel algorithm for measuring protein structure similarity that puts emphasis on high-quality modeling of local similarities of the amino acids. This is achieved by representing each amino acid by its spatial neighborhood containing close amino acids. The approach leads to good realworld results, especially for superfamily/fold classification accuracy and for precision at high recall levels where we outperform all the compared solutions. The focus on the quality of the modeling results in high computational demands of the method. We resolve this handicap be introduction of SProt access method - a modification of LAESA metric access method - that highly decreases the runtime needed for scanning large datasets of protein structures. The speedup makes SProt competitive with the best contemporary solutions not only concerning the effectiveness but also the efficiency. (en)
Title	SProt: sphere-based protein structure similarity algorithm SProt: sphere-based protein structure similarity algorithm (en)
skos:prefLabel	SProt: sphere-based protein structure similarity algorithm SProt: sphere-based protein structure similarity algorithm (en)
skos:notation	RIV/00216208:11320/11:10099650!RIV12-MSM-11320___
http://linked.open...avai/predkladatel	Matematicko-fyzikální fakulta
http://linked.open...avai/riv/aktivita	S Z
http://linked.open...avai/riv/aktivity	S, Z(MSM0021620838)
http://linked.open...iv/cisloPeriodika	Suppl. 1
http://linked.open...vai/riv/dodaniDat	2012
http://linked.open...aciTvurceVysledku	Skopal, Tomáš Hoksza, David Galgonek, Jakub
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	Univerzita Karlova v Praze / Matematicko-fyzikální fakulta
http://linked.open...dnocenehoVysledku	231690
http://linked.open...ai/riv/idVysledku	RIV/00216208:11320/11:10099650
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	structure similarity; protein; SProt (en)
http://linked.open.../riv/klicoveSlovo	SProt structure similarity protein
http://linked.open...odStatuVydavatele	GB - Spojené království Velké Británie a Severního Irska
http://linked.open...ontrolniKodProRIV	[827A8D049245]
http://linked.open...i/riv/nazevZdroje	Proteome Science
http://linked.open...in/vavai/riv/obor	IN
http://linked.open...ichTvurcuVysledku	3 (xsd:int)
http://linked.open...cetTvurcuVysledku	3 (xsd:int)
http://linked.open...UplatneniVysledku	2011
http://linked.open...v/svazekPeriodika	9
http://linked.open...iv/tvurceVysledku	Skopal, Tomáš Hoksza, David Galgonek, Jakub
http://linked.open...ain/vavai/riv/wos	000299782200020
http://linked.open...n/vavai/riv/zamer	Moderní metody, struktury a systémy informatiky
issn	1477-5956
number of pages	12 (xsd:int)
http://bibframe.org/vocab/doi	10.1186/1477-5956-9-S1-S20
http://localhost/t...ganizacniJednotka	11320
is http://linked.open...avai/riv/vysledek of	SProt: sphere-based protein structure similarity algorithm SProt: sphere-based protein structure similarity algorithm

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