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. Author manuscript; available in PMC: 2013 Oct 19.
Published in final edited form as: Biochemistry. 2012 Mar 14;51(12):2453–2460. doi: 10.1021/bi300169x

Table II.

Rosetta docking parameters

System Docking
Type		 Flags Structures
Generated		 Input Structure Plot
(Figure 4)		 Lowest
Energy		 RMSD
2PCC,
CCP & Cytc		 Global use_input_sc, ex1,
ex2aro, unboundrot		 1,000 Prepacked A. −318.2 10.2
2PCC,
CCP & Cytc		 Local
Refinement		 use_input_sc, ex1,
ex2aro, unboundrot,
docking_local_refine		 1,000 Prepacked B. −455.8 4.2
L. major,
LmP & LmCytc		 Global use_input_sc, ex1,
ex2aro, unboundrot		 10,000 Aligned over
2PCC &
Prepacked		 C. −433.9 11.6
L. major,
LmP & LmCytc		 Local
Refinement		 use_input_sc, ex1,
ex2aro, unboundrot,
docking_local_refine		 10,000 Aligned over
2PCC &
Prepacked		 D. −438.3 2.5