• Register
Forgot Password

If you have forgotten your password you can enter your email here and get a temporary password sent to your email.


Leaving Community

Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.

Forgot Password

If you have forgotten your password you can enter your email here and get a temporary password sent to your email.


Last updated April 18, 2019

Pose Predictions

Pose predictions were evaluated in terms of symmetry-corrected root-mean-square deviations (RMSD, Å) from the crystallographic poses. Stage 1A is a cross-docking challenge, while Stage 1B is a self-docking challenge. In the graphs, the pull-down menu allows display of the results for all submissions for each compound (e.g., BACE_1), the mean over all compounds (Mean over all), or the median over all compounds (Median over all). The three buttons above the menu in the graphs allow display of the RMSD values for lowest RMSD pose among the maximum of five in each submission (Closest); of the average RMSD value across all five (Average); or of the RMSD value for the top-scoring pose in each submission (Pose 1). The tables and csv files provide the statistics averaged over ligands.
BACE Stage 1A

Pose Predictions (Partials)

BACE Stage 1B

Pose Prediction (Partials)

Affinity Predictions

This section presents metrics of the ability of the predictions to correctly rank ligands by affinity. The rankings were evaluated in terms of the Kendall's τ and Spearman's ρ. Predicted binding energies for the free energy sets were additionally evaluated in terms of centered root-mean-square error (RMSEc, kcal/mol) [1] and Pearson's R. Uncertainties in these statistics (e.g., Kendall's τ Errors in the table) were obtained by recomputing them in 10,000 rounds of resampling with replacement, where, in each sample, the experimental IC50 or Kd data were randomly modified based on the experimental uncertainties. Experimental uncertainties are added to the free energy, ΔG, as a random offset δG drawn from a Gaussian distribution of mean zero and standard deviation RTln(Ierr). In this evaluation, the value of Ierr was set to 2.5.

User Submissions


BACEStage1a.zip (812M)
BACEStage1b.zip (383M)
BACEStage2.zip (786M)

Cathepsin S

CatS.zip (966M)

Protocol Files

gc4protocols.zip (700k)

Further details of these procedures and results will be provided in an overview paper in the special issue of JCAMD.

All scripts used to evaluate submissions are publicly available on Github.

(partials) indicates submissions that do not include the full set of predictions

References: [1] Gathiaka, S., Liu, S., Chiu, M. et al. J Comput Aided Mol Des (2016) 30: 651. https://doi.org/10.1007/s10822-016-9946-8

Are you sure you want to delete that component?