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Cross dj data version 3.0.18/8/2023 ![]() ![]() 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. ![]() 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. CAVER 3.0 implements new algorithms for the calculation and clustering of pathways. Herein we present a new version of CAVER enabling automatic analysis of tunnels and channels in large ensembles of protein conformations. CAVER is a software tool widely used for the identification and characterization of transport pathways in static macromolecular structures. 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. Tunnels and channels facilitate the transport of small molecules, ions and water solvent in a large variety of proteins. ![]()
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