R 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 (203 Česká republika, domácí), Antonín PAVELKA (203 Česká republika, domácí), Petr BENEŠ (203 Česká republika), Ondřej STRNAD (203 Česká republika), Jan BREZOVSKÝ (203 Česká republika, domácí), Barbora KOZLÍKOVÁ (203 Česká republika, domácí), Artur Wiktor GORA (616 Polsko, domácí), Vilém ŠUSTR (203 Česká republika, domácí), Martin KLVAŇA (203 Česká republika), Petr MEDEK (203 Česká republika), Lada BIEDERMANNOVÁ (203 Česká republika, domácí), Jiří DAMBORSKÝ (203 Česká republika, garant, domácí) a Jiří SOCHOR (203 Česká republika)

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

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

Štítky

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
Název: Analýza a vizualizace proteinových struktur
Investor: Grantová agentura ČR, Analýza a vizualizace proteinových struktur