Grand Challenge 3 Evaluations README

Files are named according to the following syntax: CatS_stage#_Pose_submission ID_LigandEval.csv.

Each csv file contains the RMSD evaluation for every submitted ligand, against every reference chain, contained within that submission ID.

The procedure for calculating RMSDs between the participant submitted ligand and crystallographic (reference) ligand was as follows:
(1) align the participant submitted protein + ligand complex onto the first chain of the crystallographic structure, using the align binding sites routine in schrodinger.
(2) evaluate RMSDs between the participant submitted pose, and reference ligand, using the MCSS routine in openeye.
(3) repeat (1)-(2) for every chain in the reference protein crystallographic structure.

Please note, given the RMSD between a ligand and a reference ligand across multiple chains, the minimum RMSD across the chains was used for GC3 statistics. For instance, if the RMSD against chain A = 2.6 ang, chain B = 2.9 ang, and chain C = 3.1 ang, the chain A = 2.6 ang RMSD would be used for statistics.

As done in prior Grand Challenge evaluations, The uncertainty in each value was assessed over 10,000 rounds of bootstrap resampling with replacement, accounting also for the experimental uncertainties. Experimental uncertainties are added to the free energy, ΔG, as a random offset δdrawn from a Gaussian distribution of mean zero and standard deviation RTln(Ierr). In this evaluation, the value of Ierr was set to 2.5.