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dxTuber: Detecting biomolecular cavities based on solvent and protein dynamics
dxTuber is the first cavity detection tool that takes into account protein and cavity dynamics using solvent and protein residence probabilities derived from molecular dynamics (MD) simulations. dxTuber supports all MD packages that VMD can process.
dxTuber results can be exported in PDB format where each cavity is an individually selectable object of coherent voxels written as pseudo atoms, each holding the residence probability information, in the form of mass-weighted solvent densities encoded as formal b-factors.
It calculates pore and tunnel profiles along principal axis, furthermore cavity volumes and solvent densities can be directly extracted from the PDB files. Based on this data cavity statistics can be obtained easily.
Quick start
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