**  Note,   This functionality is now built-in to Discovery Studio.  It is in the "General Purpose" list of protocols.

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Cleans up common problem in input protein structures in preparation for their use in other protocols, for example the Simulation protocols.

(1)Standardize atom names, insert missing atoms in residues and remove alternate conformations

(2) Insert Missing Loop Regions based on SEQRES data

(3) Optimize Short and Medium Size Loop Regions with Looper Algorithm

(4) Minimize Remaining Loop Regions

(5) Calculate pK and Protonate Structure

Note: In order make use of all steps listed above, this protocol requires MODELLER, Biopolymer, Protein Refinement and CHARMm or CHARMm Lite licenses.

Tested for DS 2.1 with PLP 6.1.6. Created by Marc Fasnacht