Summary

Rpxdock (as well as the ambitious vaporware scheme, and the conceptually related rifdock) is a multi-scale model of protein structure suited to global search of conformation space. rpxdock utilizes a novel transform-based objective function which retains some of the power of fullatom force-fields, while avoiding a costly and difficult-to-optimize fullatom model. The rpxdock model is carefully crafted to allow both pair and hierarchical decomposition of all underlying DOFs, opening the door to new optimization techniques like Hierarchical Sampling and Scoring and Hierarchical Packing. Rpxdock and related projects are currently in use in the baker lab, and seem to perform well.

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