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D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.

ABSTRACT: 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.

SUBMITTER: Parks CD 

PROVIDER: S-EPMC7261493 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

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D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.

Parks Conor D CD   Gaieb Zied Z   Chiu Michael M   Yang Huanwang H   Shao Chenghua C   Walters W Patrick WP   Jansen Johanna M JM   McGaughey Georgia G   Lewis Richard A RA   Bembenek Scott D SD   Ameriks Michael K MK   Mirzadegan Tara T   Burley Stephen K SK   Amaro Rommie E RE   Gilson Michael K MK  

Journal of computer-aided molecular design 20200123 2

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  ...[more]

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