New Features

• Scoring functions now work via a plug-in architecture. This provides several improvements:

  1. The primary scoring function and the rescoring functions can be selected at run time.

  2. The rescoring functions are now incorporated into the main DockIt executable so there are no separate rescoring programs to run. This results in a significant overall speedup in runs.

  3. The scoring function plugin system is exported in an open API which allows users to program and use their own scoring (or rescoring) functions. These functions can be used by DockIt in exactly the same way as the Metaphorics provided functions. The new functions can be mixed and matched with the provided functions at run time.

  4. The PLP and PMF scoring functions now compute derivatives so they can be used as primary scoring functions.

• PLP atom typing is now applied to cofactors and non-standard amino acids present in the protein.

• Improvements and bug fixes, particularly to the utility and analysis programs.