DARC 2.0: Improved Docking and Virtual Screening at Protein Interaction Sites
Table 1
DARC weights obtained via different approaches.
The first four parameters (c1/c2/c3/c4) refer to those used by DARC to evaluate shape complementarity (Eq 1); the last parameter (c5) is used to scale the electrostatic term, when this term is used (Eq 4). The original DARC weights were obtained by minimizing the collective RMSD for docking a series of seven ligands to their cognate receptors [22]. We also report the weights that arise from our new weight fitting approach (Enhancement #2), trained on all 25 proteins in our latest test set. Because this new approach is much faster, we were able to apply leave-one-out cross-validation to this set; here we also report the standard deviation observed among the weights trained on the 24-protein subsets. The magnitudes of the weights are not indicative of the relative importance of each term in the scoring function, since the magnitudes of the unscaled contributions vary broadly (e.g. the unscaled electrostatic term is typically much larger than the other terms, so a very small weight is needed to balance its contributions to the total score).