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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


Efficient Nearest-Neighbors

Shielding and Solvent Accessibility

Domain Detection

Conservation Analysis

Sequence Fetcher

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