DOPELoopModel reference

The DOPELoopModel class is derived from LoopModel, and is very similar in operation, except that a newer DOPE-based loop modeling protocol is used (see Selection.assess_dope()). The main differences are:

• DOPE (see Selection.assess_dope()) potential used in combination with GB/SA implicit solvent interaction (see Section 6.14).

• Lennard-Jones potential used rather than soft-sphere.

• Improved handling of ligand-loop interactions.

To use, simply use 'DOPELoopModel' rather than 'LoopModel' in your Python scripts (see Section 2.3 for examples). Note that it will be significantly slower than the regular loop modeling procedure, primarily due to the GB/SA interaction.