Provides rapid, accurate and fully automated calculation of tunnels and channels in static structures. The molecules amendable to analysis of CAVER include proteins, nucleic acids or inorganic materials. CAVER can be used either as PyMol plugin or independent application CAVER Analyst. CAVER Analyst has been designed for easy set-up of calculation, visualization of results and efficient data analysis. It can be used for both static structures and molecular ensembles from molecular dynamic simulations or NMR.
A web-based interactive application for the analysis of access/egress paths to interior molecular voids. MOLEonline 2.0 enables platform-independent, easy-to-use and interactive analyses of (bio)macromolecular channels, tunnels and pores. Results are presented in a clear manner, making their interpretation easy. For each channel, MOLEonline displays a 3D graphical representation of the channel, its profile accompanied by a list of lining residues and also its basic physicochemical properties.
A tool for the identification of high clearance pathways or corridors which represent molecular channels in the complement space of proteins. MolAxis is extremely efficient because it samples the medial axis of the complement of the molecule, reducing the problem dimension to two, since the medial axis is composed of surface patches. It is designed to analyze proteins channels, calculate pore dimensions and analyze atom accessibility.
Extracts and comprehensively analyzes all the internal volumes from input RNA and protein structures. 3V rapidly finds internal volumes by taking the difference between two rolling-probe solvent-excluded surfaces, one with as large as possible a probe radius and the other with a solvent radius (typically 1.5 A for water).
A web server that can generate contiguous conformations of a molecule along a curved tunnel inside a protein, and the binding free energy profile along the predicted channel pathway. SLITHER adopts an iterative docking scheme, which combines with a puddle-skimming procedure, i.e. repeatedly elevating the potential energies of the identified global minima, thereby determines the contiguous binding modes of substrates inside the protein.
Computes the void parts of the proteins, i.e. cavities, channels and pockets. The present approach is a variant of the alpha shapes method, with the advantage of taking into account the size and the shape of the ligand.
A highly versatile and easy-to-use tool for cavity prospection and spatial characterization. KVFinder is a geometrical-based method that has an innovative customization of the search space. It presents novel usability features, granting full customizable and highly detailed cavity prospection on proteins, alongside with a friendly graphical interface.
A program that generates a "casting" of the interior volume of the protein as dummy atoms. The use of HOLLOW significantly simplifies the generation of channel surfaces, and other interior surfaces of protein structures.
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