Documentation

AHoJ Methodology

1. The user specifies a Point of Interest (POI) in the form of a ligand, ligand-binding residue, or post-translationally modified residue in the query structure.
2. AHoJ selects the ligand(s) either directly (if the user explicitly defined the index), or by applying a distance threshold from the specified binding residue.
3. The protein binding residues (pocket) for the selected ligand are detected by applying a distance threshold.
4. The protein binding residues are mapped onto the UniProt sequence that the protein chain belongs to.
5. The available structures in the Protein Data Bank (PDB) that feature a minimum percentage of the mapped binding residues (MBRs) in their SEQRES are collected as candidate structures.
6. The query binding residues are mapped (through UniProt) onto all other candidate structures, and the query binding site (pocket) is reconstructed in each candidate structure.
7. The MBRs in the candidate structures are checked for bound ligands & metrics are collected to measure the similarity between the query pocket and each candidate pocket (chain RMSD, pocket residue RMSD, SASA, etc.).
8. Depending on the presence or absence of ligands (and considering the user settings), the candidate pockets are annotated as holo or apo, in reference to the particular query pocket.

Sequence Similarity Search

AHoJ-DB can be searched by UniProt sequence similarity. The query is either a UniProt accession (e.g. P12345, optionally with an isoform suffix like P12345-2) or a raw protein sequence (with or without a FASTA header). The query is matched with MMseqs2 against the set of unique UniProt sequences referenced by AHoJ-DB entries. Each hit row shows the number of AHoJ-DB entries containing that UniProt and a 4-chip strip summarising the AlphaFold-model apo/holo classification at the named UBS thresholds (0.3 / 0.5 / 0.7 / 1.0).

REST API

REST API Documentation

Interactive REST API browser is available here or alternatively here (redoc).