BROOD 3.0 Database
- chembl20.tgz (5.9 GB)
- chembl20.zip (5.9 GB)
Please note the above two files provide exactly the same BROOD database. The .zip format is more suitable for Windows users.
BROOD 2.0 Database
Please note that although it is compatible with BROOD 3.0, the use of this database is not recommended. It does not provide any information on the source molecule for any particular fragment.
- brood-2.0.0-database.tar.gz (3.3 GB)
OMEGA 3D Databases
- eMolecules_2017.2_maxconfs200.oeb.gz (29 GB)
- eMolecules_2017.2_maxconfs50.oeb.gz (21 GB)
- eMolecules_2017.2_maxconfs10.oeb.gz (17 GB)
- unfiltered_eMolecules_2017.2.oeb.gz (31 GB)
- KISHIDA_2016_specified_stereos_filtered_omega200.oeb.gz (5.2 GB)
- KISHIDA_2016_specified_stereos_unfiltered_omega200.oeb.gz (5.8 GB)
- KISHIDA_2016_unspecified_stereos_filtered_omega200.oeb.gz (7.9 GB)
- KISHIDA_2016_unspecified_stereos_unfiltered_omega200.oeb.gz (8.5 GB)
Please note these databases are generated with OMEGA 3.0.0. To access the Namiki databases please contact firstname.lastname@example.org. These databases are provided for our Japanese customers only.
OMEGA Fragment Library
Fragments collated from commonly used electronic databases, such as Enamine Building Blocks
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.
Spruce Loop Template Database