A Diffusion-Based Framework for Designing Molecules in Flexible Protein Pockets

Datasets for the paper: A Diffusion-Based Framework for Designing Molecules in Flexible Protein Pockets

moad.ckpt: the checkpoint file of the model trained on Binding MOAD dataset.

yuel_design.zip: source codes of YuelDesign

every_part_a.zip, every_part_b.zip: The Binding MOAD dataset.

cdk2_yueldesign.tar: the molecules generated by YuelDesign for CDK2.

cdk2_diffsbdd: the molecules generated by DiffSBDD for CDK2.

cdk2_pmdm: the molecules generated by PMDM for CDK2.

cdk2_pocket.pdb: the pocket file of CDK2.

cdk2_ref.sdf: the reference ligand file used for molecule generated with DiffSBDD.