. . "Brezovsk\u00FD, Jan" . . . . "13"^^ . . . . . "10" . "software tool; tunnel; channel; structural analysis; protein design; drug design; CAVER; dynamics"@en . "Damborsk\u00FD, Ji\u0159\u00ED" . "13"^^ . "\u0160ustr, Vil\u00E9m" . . . "RIV/00216224:14310/12:00057117" . . . . . "Kozl\u00EDkov\u00E1, Barbora" . . "14310" . "[2D830A4DD206]" . "Biedermannov\u00E1, Lada" . "Pavelka, Anton\u00EDn" . . . "CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures"@en . "CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures" . "G\u00F3ra, Artur Wiktor" . . "US - Spojen\u00E9 st\u00E1ty americk\u00E9" . "12"^^ . "\u0160ebestov\u00E1, Eva" . "126151" . "Strnad, Ond\u0159ej" . "8" . . . "000310568800009" . "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." . "CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures"@en . "Sochor, Ji\u0159\u00ED" . "CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures" . . . . . . . . "1553-7358" . "Bene\u0161, Petr" . . "10.1371/journal.pcbi.1002708" . . . "Medek, Petr" . . "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 . . "I, P(ED0001/01/01), P(ED1.100/02/0123), P(GAP202/10/1435), P(GAP503/12/0572), P(IAA401630901)" . "G\u00F3ra, Artur Wiktor" . "RIV/00216224:14310/12:00057117!RIV13-AV0-14310___" . "PLoS Computational Biology" . . "Klva\u0148a, Martin" . . . .