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GC4_overview_paper_chemrxiv.pdf (6.85 MB)

D3R Grand Challenge 4: Blind Prediction of Protein-Ligand Poses, Affinity Rankings, and Relative Binding Free Energies

submitted on 12.12.2019, 23:50 and posted on 19.12.2019, 10:58 by conor parks, Zied Gaieb, Michael Chiu, Huanwang Yang, Chenghua Shao, W. Patrick Walters, Johanna M. Jansen, Georgia McGaughey, Richard A. Lewis, Scott D. Bembenek, Michael K. Ameriks, Tara Mirzadegan, Stephen K. Burley, Rommie Amaro, Michael Gilson
The Drug Design Data Resource (D3R) aims to identify best practice methods for computer aided drug design through blinded ligand pose prediction and affinity challenges. Herein, we report on the results of Grand Challenge 4 (GC4). GC4 focused on proteins beta secretase 1 and Cathepsin S, and was run in an analogous manner to prior challenges. In Stage 1, participant ability to predict the pose and affinity of BACE1 ligands were assessed. Following the completion of Stage 1, all BACE1 co-crystal structures were released, and Stage 2 tested affinity rankings with co-crystal structures. We provide an analysis of the results and discuss insights into determined best practice methods.


Email Address of Submitting Author


University of California San Diego


United States

ORCID For Submitting Author


Declaration of Conflict of Interest

MKG has an equity interest in, and is a co-founder and scientific advisor of, VeraChem LLC; REA has equity interest in and is a co-founder and scientific advisor of Actavalon, Inc.; and PW has an equity interest in Relay Pharmaceuticals, Inc.