Dinamica molecular Informatica

caver 3.0 Tunnels and channels

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.


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