| CHOVANCOVÁ, Eva, Antonín PAVELKA, Petr BENEŠ, Ondřej STRNAD, Jan BREZOVSKÝ, Barbora KOZLÍKOVÁ, Artur Wiktor GORA, Vilém ŠUSTR, Martin KLVAŇA, Petr MEDEK, Lada BIEDERMANNOVÁ, Jiří SOCHOR and Jiří DAMBORSKÝ. CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures. PLoS Computational Biology. 2012, vol. 8, No 10, p. "nestránkováno", 12 pp. ISSN 1553-7358. Available from: https://dx.doi.org/10.1371/journal.pcbi.1002708. |
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@article{1070113,
author = {Chovancová, Eva and Pavelka, Antonín and Beneš, Petr and Strnad, Ondřej and Brezovský, Jan and Kozlíková, Barbora and Gora, Artur Wiktor and Šustr, Vilém and Klvaňa, Martin and Medek, Petr and Biedermannová, Lada and Sochor, Jiří and Damborský, Jiří},
article_number = {10},
doi = {http://dx.doi.org/10.1371/journal.pcbi.1002708},
keywords = {software tool; tunnel; channel; structural analysis; protein design; drug design; CAVER; dynamics},
language = {eng},
issn = {1553-7358},
journal = {PLoS Computational Biology},
title = {CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures},
url = {http://www.caver.cz},
volume = {8},
year = {2012}
}
TY - JOUR
ID - 1070113
AU - Chovancová, Eva - Pavelka, Antonín - Beneš, Petr - Strnad, Ondřej - Brezovský, Jan - Kozlíková, Barbora - Gora, Artur Wiktor - Šustr, Vilém - Klvaňa, Martin - Medek, Petr - Biedermannová, Lada - Sochor, Jiří - Damborský, Jiří
PY - 2012
TI - CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures
JF - PLoS Computational Biology
VL - 8
IS - 10
SP - "nestránkováno"
EP - "nestránkováno"
SN - 15537358
KW - software tool
KW - tunnel
KW - channel
KW - structural analysis
KW - protein design
KW - drug design
KW - CAVER
KW - dynamics
UR - http://www.caver.cz
N2 - 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 3.0, the tool was applied for the analysis of molecular dynamics simulation of the microbial enzyme haloalkane dehalogenase DhaA. CAVER 3.0 safely identified and reliably estimated the importance of all previously published DhaA tunnels, including the tunnels closed in DhaA crystal structures. Obtained results clearly demonstrate that analysis of molecular dynamics simulation is essential for the estimation of pathway characteristics and elucidation of the structural basis of the tunnel gating. CAVER 3.0 paves the way for the study of important biochemical phenomena in the area of molecular transport, molecular recognition and enzymatic catalysis. The software is freely available as a multiplatform command-line application at http://www.caver.cz.
ER -
CHOVANCOVÁ, Eva, Antonín PAVELKA, Petr BENEŠ, Ondřej STRNAD, Jan BREZOVSKÝ, Barbora KOZLÍKOVÁ, Artur Wiktor GORA, Vilém ŠUSTR, Martin KLVAŇA, Petr MEDEK, Lada BIEDERMANNOVÁ, Jiří SOCHOR and Jiří DAMBORSKÝ. CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures. \textit{PLoS Computational Biology}. 2012, vol.~8, No~10, p.~''nestránkováno'', 12 pp. ISSN~1553-7358. Available from: https://dx.doi.org/10.1371/journal.pcbi.1002708.
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