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Statements

Subject Item
n2:RIV%2F00216224%3A14310%2F11%3A00050643%21RIV12-GA0-14310___
rdf:type
n14:Vysledek skos:Concept
dcterms:description
Tunnels and channels facilitate the transport of small molecules, ions and water solvent in a large variety of proteins. Characteristics of individual transport pathways, including their geometry, physico-chemical properties and dynamics are instrumental for understanding of structure-function relationships of these proteins, for the design of new inhibitors and construction of improved biocatalysts. CAVER is a software tool widely used for the identification and characterization of transport pathways in static macromolecular structures. Herein we present a new version of CAVER enabling automatic analysis of tunnels and channels in large ensembles of protein conformations from molecular dynamics simulations. CAVER 3.0 implements new algorithms for calculation and clustering of pathways. Trajectories from molecular dynamic simulations serve as the inputs, while detailed characteristics and summary statistics of the time evolution of individual pathways are provided in the outputs. Tunnels and channels facilitate the transport of small molecules, ions and water solvent in a large variety of proteins. Characteristics of individual transport pathways, including their geometry, physico-chemical properties and dynamics are instrumental for understanding of structure-function relationships of these proteins, for the design of new inhibitors and construction of improved biocatalysts. CAVER is a software tool widely used for the identification and characterization of transport pathways in static macromolecular structures. Herein we present a new version of CAVER enabling automatic analysis of tunnels and channels in large ensembles of protein conformations from molecular dynamics simulations. CAVER 3.0 implements new algorithms for calculation and clustering of pathways. Trajectories from molecular dynamic simulations serve as the inputs, while detailed characteristics and summary statistics of the time evolution of individual pathways are provided in the outputs.
dcterms:title
CAVER 3.0 CAVER 3.0
skos:prefLabel
CAVER 3.0 CAVER 3.0
skos:notation
RIV/00216224:14310/11:00050643!RIV12-GA0-14310___
n14:predkladatel
n19:orjk%3A14310
n3:aktivita
n17:P
n3:aktivity
P(GAP202/10/1435)
n3:dodaniDat
n9:2012
n3:domaciTvurceVysledku
n7:4187911 n7:5901332 Góra, Artur Wiktor n7:6084559 n7:6902677 n7:2785056 n7:2475960 n7:1030175
n3:druhVysledku
n13:R
n3:duvernostUdaju
n11:S
n3:ekonomickeParametry
free on-line verze-bez poplatku
n3:entitaPredkladatele
n18:predkladatel
n3:idSjednocenehoVysledku
189324
n3:idVysledku
RIV/00216224:14310/11:00050643
n3:interniIdentifikace
Caver_3.0
n3:jazykVysledku
n6:eng
n3:klicovaSlova
software; Tunnels; channels
n3:klicoveSlovo
n8:Tunnels n8:software n8:channels
n3:kontrolniKodProRIV
[795EFA93B1AC]
n3:licencniPoplatek
n4:N
n3:lokalizaceVysledku
MU
n3:obor
n16:IN
n3:pocetDomacichTvurcuVysledku
8
n3:pocetTvurcuVysledku
13
n3:projekt
n20:GAP202%2F10%2F1435
n3:rokUplatneniVysledku
n9:2011
n3:technickeParametry
licence GNU - General public licence verison 3
n3:tvurceVysledku
Chovancová, Eva Sochor, Jiří Brezovský, Jan Damborský, Jiří Kozlíková, Barbora Medek, Petr Klvaňa, Martin Strnad, Ondřej Šustr, Vilém Pavelka, Antonín Beneš, Petr Góra, Artur Wiktor Biedermannová, Lada
n3:vlastnik
n18:vlastnikVysledku
n3:vyuzitiJinymSubjektem
n12:A
n10:organizacniJednotka
14310