DiffAb

DiffAb webserver overview

The DiffAb webserver runs the pinned c3e2966 release to redesign antibody complementarity-determining region (CDR) sequences, structures, or both. It accepts an antibody structure with optional antigen chains and supports independent CDR co-design, coordinated multi-CDR co-design, native-start optimization, fixed-backbone sequence design, and fixed-sequence structure prediction.

Each job returns the generated PDB structures, reference structures, a CDR-sequence table, the exact inference configuration, native metadata, and downloadable files. See How to use DiffAb online for input preparation, mode selection, candidate evaluation, and limitations.

Pricing

DiffAb jobs start at 50 credits. The exact quote is calculated from the selected mode, CDRs, optimization steps, and sample count before submission.

These representative quotes use the default three CDRs (HCDR1, HCDR2, and HCDR3), five samples, and optimization step 4 where applicable:

Design mode	Credits
Co-design selected CDRs independently	120
Co-design selected CDRs together (sequence + structure)	50
Optimize selected CDRs (sequence + structure)	50
Fixed backbone for selected CDRs (sequence only)	120
Predict selected CDR structures (fixed sequence)	120

Coordinated multi-CDR co-design scales with sample count. Independent co-design, fixed-backbone design, and structure prediction scale with sample count and selected CDR count. Optimization also scales with the selected optimization step totals. Chain IDs, seed controls, and renumbering do not change the quote.

Inputs

Input	Type	Required	Description
Antibody Structure or Antibody-Antigen Complex (PDB)	PDB	Yes	One .pdb or .ent file up to 50 MiB, uploaded directly or fetched from RCSB. Multi-model files use the first model. An antibody structure is required; antigen chains are optional.
Job name	string	No	Optional label used to identify the job in history.

Settings

Core settings

Parameter	Type	Default	Description
Heavy chain ID	string	Auto-detect	Optional one-character antibody heavy-chain identifier. Leave blank for automatic antibody-chain detection and Chothia renumbering.
Light chain ID	string	Auto-detect	Optional one-character antibody light-chain identifier. Leave blank for automatic detection or for a heavy-chain-only nanobody.
Design mode	enum	Co-design selected CDRs together (sequence + structure)	Select independent sequence-and-structure co-design, coordinated multi-CDR co-design, native-start optimization, fixed-backbone sequence design, or fixed-sequence structure prediction.
CDRs to design	enum	HCDR1, HCDR2, HCDR3	Select one or more of HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3. A selected loop absent from the detected antibody produces no variant for that loop.
Optimization steps	enum	4	Visible only for Optimize selected CDRs (sequence + structure). Select one or more native-start diffusion lengths from 1, 2, 4, 8, 16, 32, and 64; each selected CDR and step combination creates a separate variant.
Number of samples	integer	5	Generates 1 to 10 samples for each native variant.

Advanced settings

Parameter	Type	Default	Description
Use a random seed	boolean	false	Generates a new seed for the job. Enabling the switch hides the reproducible seed field below.
Random seed	integer	2022	Reproducible seed from 0 to 4294967295. Visible when Use a random seed is disabled.
Input is already Chothia-numbered	boolean	false	Skips DiffAb's default AbNumber and ANARCI renumbering. Enable only for a correctly Chothia-numbered structure and provide at least one antibody chain ID because source chain auto-detection is disabled in this mode.

Outputs

Artifact	Format	Description
Generated structures	PDB	Numbered designs such as H_CDR3/0000.pdb, grouped by CDR or optimization variant and shown in the structure viewer.
Prepared inference input	PDB	Exact Chothia-renumbered input used for inference when automatic renumbering is applied.
Reference structures	PDB	Native reference.pdb and variant reference files such as REF1.pdb, kept separate from generated designs.
CDR sequence table	CSV	cdr_sequences.csv with the design name and extracted HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3 sequences.
Generated structure archive	TAR.GZ	generated.tar.gz containing only the numbered generated PDB structures.
Native run metadata	JSON	metadata.json describing the DiffAb variants and native run.
Inference configuration	YAML	diffab_config.yaml containing the exact configuration used for inference.
Execution log	TXT	log.txt when the native DiffAb run produces a log.

Understanding results

The Viewer tab displays generated, prepared-input, and reference PDB files. The CDR sequences tab lists one row per generated structure with columns for the six antibody CDRs, and the Files tab provides every returned artifact for download.

Variant folders identify the CDR or optimization branch that produced a structure. Four-digit sample numbers record generation order only. DiffAb does not return a confidence, affinity, energy, or scientific ranking score.