Table 2. Proteins and known actives selected as training data.

The eight protein targets used to test the scoring function optimization approach are the overlap between the Pham set [13] and the DUD set [2]. The known ligands used for training (Nmols) are from the Pham set. Also shown are the mean physical properties for each active set. Surflex treats polar atoms as donors or acceptors if not formally charged and scales the functional term if the atoms are formally charged. The mean number of positive and negative polar atoms is shown, with the mean number of formally charged atoms in parentheses.