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RosettaDesign: an online server for performing protein design simulations

SwiftLib: on online tool for designing combinatorial libraries from degenerate codons

Ubsrd: a database of ubiquitin family structures and features

Rosetta:  macromolecular structure prediction and design (developed by a consortium of over 30 universities in the Rosetta Commons)

PyRosetta:  a python interface to Rosetta