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.
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