DeepRank-Ab dataset

First release: 1) DeepRank_Ab.tar.gz: This archive provides the training, testing, and evaluation sets for our antibody–antigen docking benchmark under the balanced sampling configuration. Directory Structure The zipped dataset (DeepRank-Ab.tar.gz) contains the following top-level folders: benchmark_train/ benchmark_test/ benchmark_eval/ Each folder contains one directory per PDB ID included in that split. Per-PDB Structure For every PDB ID, the following subdirectories are provided: 1. pdbid-selected/ Contains all sampled structures (poses) selected for this PDB complex under the balanced sampling pipeline. 2. refined/ or rigidbody Contains data generated from the refinement protocol or rigid-body docking protocol including: Clustering output Binned DockQ scores 2) DeepRank_Ab-upsampeld.tar.gz: This archive provides the training, testing, and evaluation sets for our antibody–antigen docking benchmark under the up-sampled sampling configuration. Data structure is the same as DeepRank_Ab.tar.gz. 3) af3_test_set.tar.gz: This archive contains af3_test_set. In each folder, there is an ensemble structure produced by AF3. Ranking (scoring) from AF3 is also provide. 4) reference.tar.gz This archive contains all cleaned, formatted reference structure of all antibody-antigen complexes use in this work.