2011
CAVER 3.0
CHOVANCOVÁ, Eva; Antonín PAVELKA; Petr BENEŠ; Ondřej STRNAD; Jan BREZOVSKÝ et al.Základní údaje
Originální název
CAVER 3.0
Název česky
CAVER 3.0
Autoři
CHOVANCOVÁ, Eva; Antonín PAVELKA; Petr BENEŠ; Ondřej STRNAD; Jan BREZOVSKÝ; Barbora KOZLÍKOVÁ ORCID; Artur Wiktor GORA; Vilém ŠUSTR; Martin KLVAŇA; Petr MEDEK; Lada BIEDERMANNOVÁ; Jiří DAMBORSKÝ a Jiří SOCHOR
Vydání
2011
Další údaje
Jazyk
angličtina
Typ výsledku
Software
Obor
10201 Computer sciences, information science, bioinformatics
Stát vydavatele
Česká republika
Utajení
není předmětem státního či obchodního tajemství
Označené pro přenos do RIV
Ano
Kód RIV
RIV/00216224:14310/11:00050643
Organizační jednotka
Přírodovědecká fakulta
Klíčová slova anglicky
software; Tunnels; channels
Technické parametry
licence GNU - General public licence verison 3
Změněno: 10. 4. 2012 08:30, prof. Mgr. Jiří Damborský, Dr.
Anotace
V originále
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. To illustrate the capabilities of CAVER 3.0, the tool was applied to the analysis of molecular dynamics simulation of the microbial enzyme haloalkane dehalogenase DhaA. CAVER 3 safely identified and reliably estimated the importance of all previously published DhaA pathways, including the pathways closed in DhaA crystal structures. Moreover, five examples of DhaA variants carrying substitutions in the bottleneck residues identified by CAVER 3.0 with substantially modified catalytic activity, binding affinity and kinetic stability are provided. Obtained results clearly demonstrate that analysis of molecular dynamics simulation is essential for 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 command-line application at http://www.caver.cz.
Návaznosti
| GAP202/10/1435, projekt VaV |
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