Rescoring

Rescoring programs

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PVM version

The rescoring programs are no longer necessary in DockIt 1.5 since the rescoring is now done in the main DockIt executable. scorepmf and scoreplp are still provided in case they are useful in post-processing DockIt output. Note that the scores which are given by scoreplp and scorepmf will be slightly different from those given by the PLP and PMF scoring routines in DockIt. This is because a distance cutoff is applied during scoring (or rescoring) in DockIt but no distance cutoff is used in scoreplp and scorepmf.

scorepmf

usage: cat protein.cex docked.cex | scorepmf pmf_table

scorepmf rescores molecules previously docked in "docked.cex" with PMF. Missing PMF atom types are reported as warnings and the atoms are ignored.

scoreplp

usage: cat protein.cex docked.cex | scoreplp

scoreplp rescores molecules previously docked in "docked.cex" with PLP. Missing PLP atom types are reported as warnings and the atoms are ignored.

References

PMF: I. Muegge and Y.C. Martin, J. Med. Chem., 42, 791-804 (1999).

PLP: 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).