About: CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures

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About: CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures Goto Sponge NotDistinct Permalink

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
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. (en)
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 (en)
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 (en)
skos:notation	RIV/00216224:14310/12:00057117!RIV13-AV0-14310___
http://linked.open...avai/predkladatel	Přírodovědecká fakulta
http://linked.open...avai/riv/aktivita	I P
http://linked.open...avai/riv/aktivity	I, P(ED0001/01/01), P(ED1.100/02/0123), P(GAP202/10/1435), P(GAP503/12/0572), P(IAA401630901)
http://linked.open...iv/cisloPeriodika	10
http://linked.open...vai/riv/dodaniDat	2013
http://linked.open...aciTvurceVysledku	Pavelka, Antonín Biedermannová, Lada Klvaňa, Martin Chovancová, Eva Šustr, Vilém Damborský, Jiří Medek, Petr Beneš, Petr Kozlíková, Barbora Brezovský, Jan Strnad, Ondřej Sochor, Jiří Góra, Artur Wiktor
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	126151
http://linked.open...ai/riv/idVysledku	RIV/00216224:14310/12:00057117
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	software tool; tunnel; channel; structural analysis; protein design; drug design; CAVER; dynamics (en)
http://linked.open.../riv/klicoveSlovo	CAVER protein design channel tunnel software tool drug design dynamics structural analysis
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[2D830A4DD206]
http://linked.open...i/riv/nazevZdroje	PLoS Computational Biology
http://linked.open...in/vavai/riv/obor	CE
http://linked.open...ichTvurcuVysledku	13 (xsd:int)
http://linked.open...cetTvurcuVysledku	13 (xsd:int)
http://linked.open...vavai/riv/projekt	Construction of a synthetic metabolic pathway for degradation of important environmental pollutant using protein and metabolic engineering CETOCOEN Analysis and Visualization of Protein Structures Evolution of substrate specificity in enzymes acting on xenobiotic compounds St. Anne´s University Hospital Brno - International Clinical Research Center (FNUSA-ICRC)
http://linked.open...UplatneniVysledku	2012
http://linked.open...v/svazekPeriodika	8
http://linked.open...iv/tvurceVysledku	Beneš, Petr Biedermannová, Lada Brezovský, Jan Damborský, Jiří Góra, Artur Wiktor Kozlíková, Barbora Klvaňa, Martin Medek, Petr Pavelka, Antonín Sochor, Jiří Strnad, Ondřej Šustr, Vilém Šebestová, Eva
http://linked.open...ain/vavai/riv/wos	000310568800009
issn	1553-7358
number of pages	12 (xsd:int)
http://bibframe.org/vocab/doi	10.1371/journal.pcbi.1002708
http://localhost/t...ganizacniJednotka	14310
is http://linked.open...avai/riv/vysledek of	CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures

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