Database Downloads

BROOD

BROOD 3.2 Databases

• chembl31.tar.gz (23.7 GB)
• chembl31_lite.tar.gz (9.9GB)

The database ChEMBL31 contains all possible fragments, up to three attachment points, whereas ChEMBL31_lite is curated to prioritize fragments with medicinal relevance.

BROOD 3.0 Database

• chembl20.tgz (5.9 GB)
• chembl20.zip (5.9 GB)

Please note the above two 3.0 files provide exactly the same BROOD database. The .zip format is more suitable for Windows users.

OMEGA Fragment Library

Fragments collated from commonly used electronic databases, such as Enamine Building Blocks

• omega_fragment_lib_2023.oeb.gz
• omega_fragment_lib_2020.oeb.gz

SiteHopper Databases

Available ready-to-search SiteHopper patch databases for rapid comparison of protein binding sites.

Databases of~40,000 protein-ligand binding sites, or ~300,000 potential protein binding sites, the latter identified via OEPocket and F-Pocket 4.0 The datasets were generated using ~40,000 prepared design units from roughly 21,000 PDB files.

• SiteHopper_Guide_to_Pharmacology_Patch_DB_OEv1.0.shdb (26 GB)
  
• SiteHopper_Guide_to_Pharmacology_Alternate_Sites_Patch_DB_OEv1.0.shdb (338 GB)
  

Database of SiteHopper patches based on AlphaFold2v1 structures downloaded on 10/19/2021. We utilized F-pocket and OEPocket to detect potential binding pockets. The pockets were filtered to satisfy a requirement that all residues in the identified pocket were considered a high quality prediction (prediction value in B-factor column = 100). The database contains ~106,000 patches of potential binding sites.

• AlphaFold2v1-Human-20211019_Alternate_Sites_Patch_DB_OEv1.0.shdb (67 GB)
  

SPRUCE

Spruce Loop Template Database

• rcsb_spruce_1_0_20200422.loop_db