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Statements

Subject Item
n2:RIV%2F00216224%3A14310%2F12%3A00057117%21RIV13-AV0-14310___
rdf:type
skos:Concept n17:Vysledek
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. CAVER 3.0 implements new algorithms for the calculation and clustering of pathways. A trajectory from a molecular dynamics simulation serves as the typical input, while detailed characteristics and summary statistics of the time evolution of individual pathways are provided in the outputs. To illustrate the capabilities of CAVER 3. 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. CAVER 3.0 implements new algorithms for the calculation and clustering of pathways. A trajectory from a molecular dynamics simulation serves as the typical input, while detailed characteristics and summary statistics of the time evolution of individual pathways are provided in the outputs. To illustrate the capabilities of CAVER 3.
dcterms:title
CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures
skos:prefLabel
CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures
skos:notation
RIV/00216224:14310/12:00057117!RIV13-AV0-14310___
n17:predkladatel
n18:orjk%3A14310
n3:aktivita
n12:I n12:P
n3:aktivity
I, P(ED0001/01/01), P(ED1.100/02/0123), P(GAP202/10/1435), P(GAP503/12/0572), P(IAA401630901)
n3:cisloPeriodika
10
n3:dodaniDat
n5:2013
n3:domaciTvurceVysledku
n6:3986489 n6:2475960 n6:1030175 n6:2785056 Góra, Artur Wiktor n6:5531292 n6:7676239 n6:1116304 n6:5901332 n6:6902677 n6:6875017 n6:6084559 n6:4187911
n3:druhVysledku
n11:J
n3:duvernostUdaju
n9:S
n3:entitaPredkladatele
n4:predkladatel
n3:idSjednocenehoVysledku
126151
n3:idVysledku
RIV/00216224:14310/12:00057117
n3:jazykVysledku
n19:eng
n3:klicovaSlova
software tool; tunnel; channel; structural analysis; protein design; drug design; CAVER; dynamics
n3:klicoveSlovo
n7:structural%20analysis n7:drug%20design n7:software%20tool n7:channel n7:tunnel n7:dynamics n7:CAVER n7:protein%20design
n3:kodStatuVydavatele
US - Spojené státy americké
n3:kontrolniKodProRIV
[2D830A4DD206]
n3:nazevZdroje
PLoS Computational Biology
n3:obor
n10:CE
n3:pocetDomacichTvurcuVysledku
13
n3:pocetTvurcuVysledku
13
n3:projekt
n8:IAA401630901 n8:ED0001%2F01%2F01 n8:GAP202%2F10%2F1435 n8:GAP503%2F12%2F0572 n8:ED1.100%2F02%2F0123
n3:rokUplatneniVysledku
n5:2012
n3:svazekPeriodika
8
n3:tvurceVysledku
Brezovský, Jan Damborský, Jiří Šustr, Vilém Kozlíková, Barbora Biedermannová, Lada Pavelka, Antonín Šebestová, Eva Strnad, Ondřej Sochor, Jiří Beneš, Petr Medek, Petr Góra, Artur Wiktor Klvaňa, Martin
n3:wos
000310568800009
s:issn
1553-7358
s:numberOfPages
12
n20:doi
10.1371/journal.pcbi.1002708
n13:organizacniJednotka
14310