About: Finding Cavities in Molecule

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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	In recent years, biochemistry is gaining more and more attention. The research involves analysis of large molecules, such as proteins. One of many properties we can study are molecular cavities, where cavity is understood as a free space inside a molecule. As we are usually interested only in a certain subset of cavities, the common approach is to use a spherical probe of a given radius to find the cavities. The probe can be imagined as a sphere which we try to slip through the molecule. In this paper we discuss an algorithm to find inner cavities in a molecule for a given size of the probe. The algorithm has a preprocessing stage where an additively weighted Voronoi diagram of a molecule is computed. This diagram is then used to accomplish the task of finding cavities for varying probe sizes. The algorithm presented proved to be very fast for a probe with a variable size. The implementation shows it is able to operate in real-time even on large structures, such as the Thermus Thermophilus 70S ribosome (PDB ID 3OH5, approximately 87 000 atoms). In recent years, biochemistry is gaining more and more attention. The research involves analysis of large molecules, such as proteins. One of many properties we can study are molecular cavities, where cavity is understood as a free space inside a molecule. As we are usually interested only in a certain subset of cavities, the common approach is to use a spherical probe of a given radius to find the cavities. The probe can be imagined as a sphere which we try to slip through the molecule. In this paper we discuss an algorithm to find inner cavities in a molecule for a given size of the probe. The algorithm has a preprocessing stage where an additively weighted Voronoi diagram of a molecule is computed. This diagram is then used to accomplish the task of finding cavities for varying probe sizes. The algorithm presented proved to be very fast for a probe with a variable size. The implementation shows it is able to operate in real-time even on large structures, such as the Thermus Thermophilus 70S ribosome (PDB ID 3OH5, approximately 87 000 atoms). (en)
Title	Finding Cavities in Molecule Finding Cavities in Molecule (en)
skos:prefLabel	Finding Cavities in Molecule Finding Cavities in Molecule (en)
skos:notation	RIV/49777513:23520/12:43915229!RIV13-GA0-23520___
http://linked.open...avai/riv/aktivita	P S
http://linked.open...avai/riv/aktivity	P(GAP202/10/1435), S
http://linked.open...vai/riv/dodaniDat	2013
http://linked.open...aciTvurceVysledku	Jirkovský, Lukáš
http://linked.open.../riv/druhVysledku	O - Ostatní výsledky nezařaditelné do žádného z výše uvedených druhů výsledku
http://linked.open...iv/duvernostUdaju	S - Úplné a pravdivé údaje nepodléhající ochraně podle zvláštních právních předpisů
http://linked.open...titaPredkladatele	Západočeská univerzita v Plzni / Fakulta aplikovaných věd
http://linked.open...dnocenehoVysledku	136589
http://linked.open...ai/riv/idVysledku	RIV/49777513:23520/12:43915229
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	additively weighted Voronoi diagram; molecule analysis; molecular cavity (en)
http://linked.open.../riv/klicoveSlovo	additively weighted Voronoi diagram molecular cavity molecule analysis
http://linked.open...ontrolniKodProRIV	[E7E26E02F4B0]
http://linked.open...in/vavai/riv/obor	IN
http://linked.open...ichTvurcuVysledku	1 (xsd:int)
http://linked.open...cetTvurcuVysledku	1 (xsd:int)
http://linked.open...vavai/riv/projekt	Analysis and Visualization of Protein Structures
http://linked.open...UplatneniVysledku	2012
http://linked.open...iv/tvurceVysledku	Jirkovský, Lukáš
http://localhost/t...ganizacniJednotka	23520

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