Structural Proteomics Application Development Environment
The Structural Proteomics Application Development Environment (SPADE) is a cross-platform biomolecular structure analysis and visualization toolkit. SPADE is the start of a protein engineering tool I am personally interested in, and its design can give a head start to other structure biology algorithm engineers.
SPADE loads Applications into the tabbed space below the viewer, for example SequencePad, which visualizes evolutionary calculations to discriminate subtleties like protein-protein interfaces. RAVE is a chemical probing suite supporting experimental verification of predicted structural models. SPADE was built to host Molnir, a genetic algorithm-based hybrid protein structure modeling algorithm.
There are many conveniences for programmers: surface and solvent accessibility calculators, a multi-feature dynamic programming routine, and a hydrogen bond calculator. There is a constraints-free multiple structure alignment algorithm that works on even remote structures. There's more in there and more to come.
SPADE and SequencePad are available under a BSD licence. SPADE can be cited as:
Deacon J. Sweeney, Gerald M. Alter, and Michael L. Raymer: Introducing SPADE, the Structural Proteomics Application Development Environment. Ohio Collaborative Conference on Bioinformatics (OCCBIO), 2-4 June 2008, University of Toledo.
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