Scoring functions

• PMF (Potential of Mean Force)
  Atomtypes assigned by SMARTS rules; need to rederive PMF with more rational and consistent set of atomtypes. Problems with insufficient data in PDB for some atomtypes...
   
• PLP (Piecewise Linear Potential)
  D.K. Gehlhaar, G.M. Verkhiver, P.A. Reijto et al Chem. Biol., 2, 317-324 (1995).
  Simple, fast function may be more suitable than Lennard-Jones + electrostatics for optimization.
   
• ChemScore
  C.A. Baxter, C.W. Murray, D.E. Clark, et al Proteins, 33, 367-382 (1998)
  M.D. Eldridge, C.W. Murray, T.R. Auton, et al J. Comp-Aided Mol. Design, 11, 425-445 (1997).
  Empirical function fit by multiple linear regression.

 
• Consensus Scoring
  P. Charifson, P. Walters, et al (Fall '99 ACS, Spring '99 DOCK Users' Group mtg).
  Simple consensus voting approach.