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2018-11-27 - Submissions are now being accepted. Note: structure based scoring files that exceed 20M will likely not work for now. In the meantime, please upload your file to a public server like box.com, google drive and email us the download link. In it's place, please upload a smaller version to the D3R website that we can manually replace.
2018-11-26 - Template and example files are ready for download
2018-10-29 - Please note that the CatS ligands numbering in the free energy and scoring sets are offset by one.
A sharp-eyed participant noticed that the names of the ligands in the CatS free energy sets don't match those in the full scoring set. Please keep the naming as is; we will account for the discrepancy in the evaluation process.
Note: No attempt was made to set appropriate starting conformations or optimal protonation or tautomer states for the ligands, or to generate alternative tautomer states. It is up to you to choose and set these states for your calculations.
The cathepsins constitute an 11-member family of proteases involved in protein degradation. Cathepsin S is highly expressed in antigen-presenting cells, where it degrades major histocompatibility complex class II (MHC II)-associated invariant chain. CatS is a candidate target for regulating immune hyper-responsiveness, as the inhibition of CatS may limit antigen presentation1-3.
This data set comprises a follow-on challenge to GC3, consisting of non-peptidic, non-covalent, small molecule inhibitors across a three order of magnitude range (nM to μM) of IC50s for CatS. Specifically, we provide 459 CatS inhibitors for affinity prediction, and 39 molecules for free energy prediction. This dataset was kindly donated by Janssen. Please note the affinity values from this set were measured against a C25S CatS mutant.
For details of the binding assays, we were referred to publications from the Janssen group, which describe the following binding assays conditions4