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.
Related Articles
MD 2AA2 with AS4 (aldosterone) equilibration
Posted on Author SCOTTxRT
Paso de equilibration logrado. próximamente paso de producción. Para luego generar SMD (steered molecular dynamics)
CLC Sequence Viewer
Posted on Author SCOTTxRT
https://www.qiagenbioinformatics.com/products/clc-sequence-viewer/
(Chemistry at HARvard Macromolecular Mechanics)
Posted on Author SCOTTxRT
CHARMM Es un programa de simulación molecular aplicable a una gran variedad de sistemas conformados por cantidades considerables de partículas, […]