SPADE

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 scientists and 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 powerful molecular viewer, fold recognition, electroastatics, a hydrogen bond calculator, domain decomposition, and template-free multiple-superposition. 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.