CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures.

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 relat...

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Autores principales:	Eva Chovancova, Antonin Pavelka, Petr Benes, Ondrej Strnad, Jan Brezovsky, Barbora Kozlikova, Artur Gora, Vilem Sustr, Martin Klvana, Petr Medek, Lada Biedermannova, Jiri Sochor, Jiri Damborsky
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/291f1b72633147e3a03d80fd1180ac09
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spelling	oai:doaj.org-article:291f1b72633147e3a03d80fd1180ac092021-11-18T05:52:47ZCAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures.1553-734X1553-735810.1371/journal.pcbi.1002708https://doaj.org/article/291f1b72633147e3a03d80fd1180ac092012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23093919/pdf/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Tunnels 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.Eva ChovancovaAntonin PavelkaPetr BenesOndrej StrnadJan BrezovskyBarbora KozlikovaArtur GoraVilem SustrMartin KlvanaPetr MedekLada BiedermannovaJiri SochorJiri DamborskyPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 8, Iss 10, p e1002708 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Eva Chovancova Antonin Pavelka Petr Benes Ondrej Strnad Jan Brezovsky Barbora Kozlikova Artur Gora Vilem Sustr Martin Klvana Petr Medek Lada Biedermannova Jiri Sochor Jiri Damborsky CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures.
description	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.
format	article
author	Eva Chovancova Antonin Pavelka Petr Benes Ondrej Strnad Jan Brezovsky Barbora Kozlikova Artur Gora Vilem Sustr Martin Klvana Petr Medek Lada Biedermannova Jiri Sochor Jiri Damborsky
author_facet	Eva Chovancova Antonin Pavelka Petr Benes Ondrej Strnad Jan Brezovsky Barbora Kozlikova Artur Gora Vilem Sustr Martin Klvana Petr Medek Lada Biedermannova Jiri Sochor Jiri Damborsky
author_sort	Eva Chovancova
title	CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures.
title_short	CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures.
title_full	CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures.
title_fullStr	CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures.
title_full_unstemmed	CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures.
title_sort	caver 3.0: a tool for the analysis of transport pathways in dynamic protein structures.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/291f1b72633147e3a03d80fd1180ac09
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CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures.

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