SB2021 Docking Database is a molecular docking validation dataset released by Rizzo Lab1 . However, the attached mol2 ligang files may cause many errors, therefore we used Flare V72 to check and fix the ligand structures.
- ligand.tar.gz: co-crystal ligand structure in SDF format
- prot.tar.gz: co-crystal protein structure in PDB format. Pyflare was used to prepare the protein and the co-crystal ligand was extracted:
- id.lst: list of all systems
pyflare proteinprep.py -x 121p_ref.sdf ../prot/121p.pdb >> 121p_prot.pdb
Download link: prot.tar.gz
- 2024-01-22. Remove PDB 1ITV from data set because the ligand is a sulfate anion.
- 2024-01-21. Release ligand data set in SDF format.
- SB2021 Docking Database. Rizzo Lab. (Jan 21, 2024 accessed). https://ringo.ams.stonybrook.edu/index.php/SB2021.v1
- Flare V7. https://www.cresset-group.com/software/flare