AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility
Fig 10
Impact of down-weighting the receptor internal energy.
A) and B) Sorted ranks of the correct docked solutions without scaling the receptor energy (blue) and with a scaling factor of 1/NFS (green) where NFS is the number of flexible receptor side-chains, for the SEQ17 and CDK2 FS12 cross-docking calculations respectively. Overall down-weighting the receptor energy improves the rank of the lowest-energy correct solution. The top horizontal line (Rank 51) in the plots represents data points that did not find the solution in the 50 docking runs. C) and D) Distributions of improvements in receptor-ligand interaction energies (ER-L) in kcal/mol, when the internal energy of the receptor is down-weighted in the scoring functions for SEQ17 and the CDK2 FS12 calculation respectively.