. "13"^^ . "free on-line verze-bez poplatku" . "RIV/00216224:14310/11:00050643!RIV12-GA0-14310___" . "software; Tunnels; channels"@en . . . . . . "CAVER 3.0" . . "G\u00F3ra, Artur Wiktor" . "Chovancov\u00E1, Eva" . . "Sochor, Ji\u0159\u00ED" . . . "14310" . . "Brezovsk\u00FD, Jan" . "Damborsk\u00FD, Ji\u0159\u00ED" . . "Kozl\u00EDkov\u00E1, Barbora" . . "Medek, Petr" . "Klva\u0148a, Martin" . "MU" . . "P(GAP202/10/1435)" . . "189324" . "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." . "RIV/00216224:14310/11:00050643" . . "[795EFA93B1AC]" . "licence GNU - General public licence verison 3" . . "Strnad, Ond\u0159ej" . . . "\u0160ustr, Vil\u00E9m" . . "Pavelka, Anton\u00EDn" . "Bene\u0161, Petr" . "G\u00F3ra, Artur Wiktor" . . "Caver_3.0" . "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."@en . . "CAVER 3.0"@en . . "CAVER 3.0" . "Biedermannov\u00E1, Lada" . "8"^^ . "CAVER 3.0"@en . . .