TL;DR
Predict antibody-antigen complexes from sequences and inspect ipTM, contact residues, BSA, pDockQ, PDBs, and CSV exports.
Use it / Skip it
This is the primary structural scoring surface. It turns a binder sequence plus antigen into a job record that can be reopened, exported, compared, and used by CAR Interface Assessment.
Use when
You have one or many antibody sequences and need a structure-level readout against a target antigen.
Don't use for
Do not use it as final affinity truth or specificity proof. Use it to prioritize experiments and follow up with wet-lab assays.
Inputs
- Antibody input
- Single sequence or batch list; jobs can be named for later search.
- Antigen input
- Sequence, RCSB PDB code, uploaded PDB with explicit target-chain selection, or UniProt-style target input.
- Backend
- Internal GPU is the standard default; API backend exists for selected cases.
- Contact cutoff
- Distance threshold for residue contact extraction.
Outputs
- Predicted complex
- Downloadable PDB and in-page 3D viewer.
- Interface metrics
- ipTM, contacts, epitope/paratope residues, BSA, pDockQ, and affinity lookup when matched.
- Exports
- Per-job CSV, contact CSV, batch exports, and job table downloads.
Walkthrough
1. Paste the antibody sequence or batch
Paste the antibody sequence or batch. Give the run a name if it will be shared.
2. Enter the antigen
Enter the antigen. For a local complex PDB, upload it, select only the target antigen chain(s), and remember that Interface extracts sequence and re-predicts the complex rather than fixing the uploaded coordinates.
3. Submit and wait for polling
Submit and wait for polling. Running jobs stay selectable in the job strip.
4. Inspect the completed job
Inspect the completed job. Start from metrics, then review epitope/paratope contacts and PDB.
5. Use Interface Jobs or Compare when you need bulk export or head-to-head overlay
Use Interface Jobs or Compare when you need bulk export or head-to-head overlay.
Under the hood
- Standard jobs are persisted and listed through Interface job APIs.
- OpenDDE is available as a Beta entry and uses the dedicated self-hosted OpenDDE ABAG backend; important candidates should still be cross-checked with Boltz-2 or AlphaFold 3.
- Batch submission dispatches multiple antibody jobs while preserving batch naming.
Worked example
Pitfalls
- A complex PDB must be narrowed to the intended antigen chain(s); leaving every chain selected can submit the original antibody/receptor chains as antigen.
- Uploaded PDB coordinates are used for chain/sequence extraction only. Interface is sequence-based complex prediction, not rigid docking against the uploaded receptor coordinates.
- ipTM can under-call antibody-antigen interfaces. Read it with BSA, contacts, PAE/contact context, and known biology.
- Completed jobs have exportable artifacts; queued/running/failed jobs intentionally show blanks for those columns.
- Batch names help later triage. Anonymous jobs become hard to find once the table grows.