In release 1.5 of DockIt, it is now possible to specify the scoring (and rescoring) functions used when the dock program is run. There are three built in functions

dockscore: This is the default DockIt score. It is a molecular mechanics based scoring function
pmfscore: Potential of Mean Force. This is a statistical potential derived from the geometry of protein-ligand crystal structures (I. Muegge and Y.C. Martin, J. Med. Chem., 42, 791-804 (1999)).
plpscore: Piecewise Linear Potential. This is a simplified potential whose parameters are fit to protein-ligand structures and binding data (D.K. Gehlhaar, G.M. Verkhiver, P.A. Reijto, C.J. Sherman, D.B. Fogel, L.J. Fogel, S.T. Freer, Chem. Biol., 2, 317-324, (1995)).

Each of these functions can be selected to be used as the primary scoring function or as rescoring functions. Rescoring functions are used to calculate a score for each docked conformation of a ligand without further optimization. There can be one primary scoring function (which is used in the optimization of ligand docking) and any number of rescoring functions used during a DockIt run. The selections are made in CMD.CEX. The default corresponds to the following set of parameters in CMD.CEX:

/SCORE_FUNCTION<DOCKSCORE, dockscore, score.so, DockIt Score>
/RESCORE_FUNCTIONS<PLPSCORE, plpkscore, scoreplp.so, PLP Score; PMFSCORE, pmfscore, scorepmf.so, PMF Score>

/SCORE_FUNCTION<PLPSCORE, plpscore, scoreplp.so, PLP Score>
/RESCORE_FUNCTIONS<DOCKSCORE, dockscore, score.so, DockIt Score; PMFSCORE, pmfscore, scorepmf.so, PMF Score>

It is possible to write new scoring functions which plug into DockIt and can be used in place of or in addition to the supplied functions.

Scoring Function Plug-ins