From 6c858de5266953e88dc0facebbb7d044b2561552 Mon Sep 17 00:00:00 2001 From: Alex Morehead Date: Sat, 8 Feb 2025 19:37:56 -0600 Subject: [PATCH] Update CHANGELOG --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9682f06..194b189 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,7 +6,7 @@ - Added the new centroid RMSD and PLIF-EMD/WM metrics - Added a failure mode analysis notebook - Introducing DockGen-E, a new version of the DockGen benchmark dataset featuring enhanced biomolecular context for docking and co-folding predictions - namely, now all DockGen complexes represent the first (biologically relevant) bioassembly of the corresponding PDB structure -- For the single-ligand datasets (i.e., Astex Diverse, PoseBusters Benchmark, and DockGen), now providing each baseline method with primary *and cofactor* ligand SMILES strings for prediction, to enhance the biomolecular context of these methods' predicted structures - as a result, for these single-ligand datasets, now the predicted ligand *most similar* to the primary ligand (in terms of both Tanimoto and structural similarity) is selected for scoring +- For the single-ligand datasets (i.e., Astex Diverse, PoseBusters Benchmark, and DockGen), now providing each baseline method with primary *and cofactor* ligand SMILES strings for prediction, to enhance the biomolecular context of these methods' predicted structures - as a result, for these single-ligand datasets, now the predicted ligand *most similar* to the primary ligand (in terms of both Tanimoto and structural similarity) is selected for scoring (which adds an additional layer of challenges for baseline methods) - Updated Chai-1's inference code to commit `44375d5d4ea44c0b5b7204519e63f40b063e4a7c`, and ran it also with standardized (paired) MSAs - Replaced all AlphaFold 3 server predictions of each dataset's protein structures with predictions from AlphaFold 3's local inference code - Pocket-only benchmarking has been deprecated