Loop optimization
Keywords: manual

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Loop optimization

MODELLER has several loop optimization methods, which all rely on scoring functions and optimization protocols adapted for loop modeling [Fiser et al., 2000]. They are used to refine loop regions, either automatically after standard model building, or manually on an existing PDB file.

Subsections

- Automatic loop refinement after model building
- Defining loop regions for refinement
- Refining an existing PDB file