This section of the User Guide describes the post-registration structure analyses that are carried out in 3decision, and how to use 3decision API endpoints to launch them.
The main enpoints described in this section are:
/sequence-mapping/pocket-detection/ligand-cavity-overlap/pocket-features/interaction-registrationUpon registration into 3decision, all structures (experimental and in silico; public and proprietary) undergo the following post-registration analyses:
All the post-registration analyses are automatically triggered upon registration of structures in the 3decision database.
The user can re-launch each analysis individually from the 3decision REST API, using the single endpoints.
The only requirements needed to launch these analyses are:
access structure on the structure you want to reprocess.In the following sections, the analyses available from the 3decision REST API are described. They are all under the REST API Swagger category: Structure Analysis.
The protein chain sequence mapping is triggered by the API endpoint: POST /sequence-mapping.
This analysis allows to map a biomolecule sequence to the structure chains.
To retrieve the status and result of the chain mapping, you can use the API endpoint: GET /sequence-mapping/{externalCode}.
The POST /sequence-mapping endpoint request body requires the following:
chains (optional): define the biomolecule code for each protein chain. For public structures, the sequence mapping information is automatically retrieved from the structure file (DBREF for pdb files, _struct_ref_seq for PDBx/mmCIF files). For private structures, if a sequence mapping is provided in the payload, it will be used instead of the information obtained from the structure file content. Providing a custom sequence mapping is not allowed on public structures.external code: for public structures, the 4-digits PDB code; for propritary structures, the 6-digits code.commit: trueThe pocket indexing in 3decision is composed of three different analyses, that use three distinct endpoints:
POST/ pocket-detection/{externalCode}POST/ ligand-cavity-overlap/{externalCode}POST/ pocket-features/{externalCode}Launching any of these endpoints updates the pocket-related associated data to the structure in the 3decision database and may affect the output from other 3decision features, such as Pocket Similarity Search.
The endpoint POST/ pocket-detection/{externalCode} launches an analysis that detect pockets on the surface of the protein structure.
The pocket detection algorithm is based on fpocket (related paper) which identifies two types of pockets: explicit and implicit. An explicit pocket is defined by the presence of a ligand, while an implicit pocket is detected in the protein agnostically (without taking into account the ligand).
When pocket detection is performed, already existing structure pockets are updated (deleted, then newly registered) in the 3decision database.
To retrieve the status and result of the pocket detection, you can use the API endpoint: GET /pocket-detection/{externalCode}.
The pocket-detection analysis triggers the following analyses:
ligand-cavity-overlappocket-featuresinteraction-registrationWarning: for structures with more than 50,000 atoms, only explict pockets are detected.
The endpoint POST/ ligand-cavity-overlap/{externalCode} submits an analysis that calculates ligand and cavity overlap on a structure, where:
To retrieve the status and result of the ligand and cavity overlap, you can use the API endpoint: GET /ligand-cavity-overlap/{externalCode}.
The endpoint POST/ pocket-features/{externalCode} launches an analysis that characterizes pocket features for each binding site of the structure. The pocket features are calculated for pockets having at least 30 alpha spheres or any ligand.
For each residue in the pocket, physico-chemical features are identified, and their contribution to the accessible surface area of the pocket is assessed. The presence and absence of each feature are encoded in a 5-bit binary vector (fingerprint, 1 if present, 0 if not) for: HBA, negatively charged, HBD, positively charged, aromatic features.
To retrieve the status and result of the pocket features calculation, you can use the API endpoint: GET /pocket-features/{externalCode}.
The endpoint POST /interaction-registration/{externalCode} submits the detection of Protein-Ligand interactions on the specified structure.
When interaction registration analysis is performed, newly detected interactions are registered in the database, while previously existing ones are kept.
Registering new protein-ligand interactions updates the associated data to the structure in the 3decision database and may affect the output from other 3decision features, such as Interaction Search.
To retrieve the status and result of Protein-Ligand interactions calculation, you can use the API endpoint: GET /interaction-registration/{externalCode}.
Warning: for structures with more than 50,000 atoms interactions are not detected.