Tools

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Tools available in the SPADE download include a molecular viewer, a sequence alignment algorithm capable of fold-recognition searches, and a fully-automated multiple-structure alignment toolkit. SPADE MolecularSystem class objects calculate hydrogen bonds, visible surfaces, and atom or residue solvent accessibility, provide undo/redo functionality, and carry graphical data for the molecular viewer so that rendering is easily saved with project data. A pseudo-sidechain calculator was constructed that reduces the complexity of many spatial algorithms, and a built-in search algorithm rapidly queries atoms and residues for others in close proximity. These tools are available at the SPADE command prompt and will be documented here.


Molecular System


Molecular Viewer


Structure Alignment


Sequence Alignment


Proton-Related


Efficient Nearest-Neighbors


Shielding and Solvent Accessibility


Domain Detection


Conservation Analysis


Sequence Fetcher


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