About PepPCDB
Sequence Annotation Rules
Portal-level notes for interface annotation semantics, download APIs, and community feedback.
Legend Details
In Interface view, markers are embedded directly on residue characters.
| Marker | Meaning | Render Rule |
|---|---|---|
| A | MASK contact residue | Character boxed if mask position is `-`. |
| A | SS = H (Helix) | Text color by secondary structure class. |
| A | SS = E (Beta) | Text color by secondary structure class. |
| A | SS = C (Coil) | Text color by secondary structure class. |
| A | NONSTD MOD | Dotted underline and hover tooltip with mod type + position. |
Community Feedback
If you find issues, missing annotations, or opportunities to improve PepPCDB, please open a
GitHub issue
or contact zhaisilong@outlook.com.
We welcome community input to help improve and expand the database.
Quick Download API
The public API surface is limited to quick download endpoints. Browser search and detail endpoints are internal page APIs. The hosted site uses the /peppcdb prefix; root-path deployments use the same endpoints without that prefix.
| Endpoint | Output | File Naming |
|---|---|---|
GET /peppcdb/api/download/{entry_key}.zip |
All source files for one entry. | {pdb_id}.zip |
GET /peppcdb/api/download/{entry_key}/{pdb_id}.cif |
mmCIF coordinate file for one entry. | {pdb_id}.cif |
GET /peppcdb/api/download/{entry_key}/{pdb_id}_annotations.json |
Peptide chain annotations, including non-standard residue and cyclic metadata. | {pdb_id}_annotations.json |
GET /peppcdb/api/download/{entry_key}/{pdb_id}_interface.jsonl |
Pair-level interface records for one entry. | {pdb_id}_interface.jsonl |
GET /peppcdb/api/download/{entry_key}/{pdb_id}_function.json |
Generated 2-space JSON merging peptide function annotations, affinity values, target tags, and linked target-card records. | {pdb_id}_function.json |
GET /peppcdb/api/download/{entry_key}/function.json |
Compatibility alias for generated function JSON. | {pdb_id}_function.json |
Download API requests are limited to 100 requests per client IP per hour.
Roadmap / TODO
Development Log
| Date | Update | Note |
|---|