The AbDb data set, a compilation of antibodies extracted from the PDB with standard numbering schemes applied and redundancy information.
We have been performing a complete rewrite of the AbDb code as updating became impractical using the old code. Undfortunately this has taken a lot longer than we had hoped. Consequently the searchable data and split datasets available here here have not been updated since 26th July 2019!
Everything is now complete with the exception of populating the web interface. We are now supplying a snapshot of data from July 2024. This is provided as a ZIP file. For each Fv, the ZIP file contains files with extensions .kab (Kabat numbered), .cho (Chothia numbered), .mar (Martin numbered), and .faa (a FASTA sequence file). Filenames contain a P after the entry name (e.g. 1yqv_0P) to indicate a protein or peptide antigen, H to indicate a hapten, N to indicate a nucleotide. Some entries contain more than one of these (e.g. 1zea_0PH).
The ZIP file also contains the file AbClusters.txt which lists the redundant clusters. Each line represents a set of the same (redundant) antibody and contains an entry of the form:
xxxx:yyyy
where xxxx is a comma-separated list of free antibodies and yyyy is a comma-separated list of bound antibodies. Either xxxx or yyyy may be missing if there are only unbound or only bound antibodies.
For example:
3u36_0,3u36_3,3u36_2,3u36_1:
is a set of unbound antibodies having the same sequence (in this case from the same PDB file).
:3u2s_1PH,3u4e_0PH,3u4e_1PH,3u2s_0PH
is a set of bound antibodies having the same sequence (in this case from two PDB files).
1hzh_0,1hzh_1:2ny7_0PH,5vn8_2PH,5vn8_0PH,1n0x_0P,5vn8_1PH,3ru8_0P,8sxi_1P,1n0x_1P,8sxi_0P,8sxi_2P
is a set of two unbound antibodies (from one PDB file) and 10 bound antibodies (from 5 PDB files).
| Complex with Antigen Type | ||||
|---|---|---|---|---|
| Numbering | Protein | Non-protein | Free antibodies | Complete Dataset |
| Kabat | All / NR | All / NR | All / NR | All / NR |
| Individual | Individual | Individual | Individual | |
| Chothia | All / NR | All / NR | All / NR | All / NR |
| Individual | Individual | Individual | Individual | |
| Martin | All / NR | All / NR | All / NR | All / NR |
| Individual | Individual | Individual | Individual | |
| Redundant Antibody List | Download | Download | Download | Download |
| Free Antibody/Complex List | Free Antibodies/Complexes | |||
| Complex with Antigen Type | ||||
|---|---|---|---|---|
| Numbering | Protein | Non-protein | Free antibodies | Complete Dataset |
| Kabat | All / NR | All / NR | All / NR | All / NR |
| Individual | Individual | Individual | Individual | |
| Chothia | All / NR | All / NR | All / NR | All / NR |
| Individual | Individual | Individual | Individual | |
| Martin | All / NR | All / NR | All / NR | All / NR |
| Individual | Individual | Individual | Individual | |
| Redundant Antibody List | Download | Download | Download | Download |
| Free Antibody/Complex List | Free Light/Complexed Light | |||
| Complex with Antigen Type | ||||
|---|---|---|---|---|
| Numbering | Protein | Non-protein | Free antibodies | Complete Dataset |
| Kabat | All / NR | All / NR | All / NR | All / NR |
| Individual | Individual | Individual | Individual | |
| Chothia | All / NR | All / NR | All / NR | All / NR |
| Individual | Individual | Individual | Individual | |
| Martin | All / NR | All / NR | All / NR | All / NR |
| Individual | Individual | Individual | Individual | |
| Redundant Antibody List | Download | Download | Download | Download |
| Free Antibody/Complex List | Free Heavy/Complexed Heavy | |||
| Datasets | Complex Type | Processed PDB Files | Resultant Antibodies | Non-Redundant Antibodies |
|---|---|---|---|---|
| Complete Antibody | Protein | 1694 | 3000 | 1205 |
| Non-protein | 361 | 489 | 259 | |
| Free Antibody | 915 | 1536 | 810 | |
| Complete Dataset | 2894 | 5025 | 1924 | |
| Light Chains | Protein | 9 | 14 | 6 |
| Non-protein | 1 | 1 | 1 | |
| Light Only | 97 | 236 | 61 | |
| Complete Dataset | 107 | 251 | 66 | |
| Heavy Chains | Protein | 246 | 466 | 190 |
| Non-protein | 13 | 36 | 14 | |
| Heavy Only | 102 | 198 | 102 | |
| Complete Dataset | 347 | 700 | 277 |
The following statistics show the type and number of unprocessed antibody related structures that are not present in AbDb
| Fc Fragments | Numbering Failed | Superseded | Single Chain Antibody (scFVs) |
|---|---|---|---|
| 239 | 168 | 13 | 102 |
List of antibodies that failed the numbering
List of antibodies bound to multiple antigens
List of single chain antibodies (scFVs)
List of chain mapping information for all structures in AbDb