DeepRank-Ab

DeepRank-Ab webserver overview

DeepRank-Ab 1.0.2 scores antibody-antigen and nanobody-antigen complex models without requiring a reference structure. It returns predicted DockQ scores, ranked models, and flags for heavy-light chain contacts and potential steric clashes.

Pricing

Runs cost 27 credits per minute of measured runtime. The minimum reservation is 27 credits, not a minimum final charge. Completed runs are charged in proportion to elapsed time, rounded up to a whole credit; unused reserved credits are returned. Set a spending limit before submission. Each batch job is metered separately.

Inputs

Input	Accepted values	Details
Complex structure	.pdb, .ent, .cif, .mmcif	A complex containing the antibody or nanobody and its antigen; maximum 50 MiB per file.
Ensembles	Multiple models in one structure file	Each model is scored within the same job.
Batch	Up to 10 structure files	Each file runs as a separate job. Uploads, saved files, ZIP batches and RCSB PDB-code fetching use the shared input controls.

CIF/mmCIF files must be convertible to PDB while preserving model, chain, residue and atom identities, alternate conformations, coordinates, occupancy and temperature factors. Files that cannot preserve these fields are rejected. The original CIF and converted PDB remain separate downloads.

Filenames should contain letters, such as complex_001.pdb; purely numeric names such as 001.pdb can fail during result processing. A scoring run has a 25-minute execution limit.

Settings

Parameter	Type	Default	Description
Complex type (complex_type)	enum	auto	auto uses automatic chain detection; antibody requires heavy, light and antigen chain IDs; nanobody specifies that no light chain is present.
Heavy / binder chain (heavy_chain_id)	string	Auto-detect (blank)	Optional chain ID override; required in antibody mode. Automatic detection uses ANARCI.
Light chain (light_chain_id)	string	Auto-detect (blank)	Optional chain ID override; required in antibody mode and hidden in nanobody mode.
Antigen chain (antigen_chain_id)	string	Auto-detect (blank)	Optional single chain ID override; required in antibody mode. Automatic detection includes and merges multiple antigen chains.

Auto-detect supports partial overrides. When both heavy and antigen chains are specified, leaving the light chain blank means no light chain, rather than automatic light-chain detection. Antibody mode requires all three chain IDs. Nanobody mode always uses no light chain.

Outputs

The Predictions table lists models in descending predicted DockQ order and supports copying and CSV download. Downloads also retain the generated result files:

Download	Contents
*_predictions.csv	Model identifiers, predicted DockQ scores and both quality flags.
*_predictions.hdf5	Prediction data and associated metadata.
Structure files	Original structures, split ensemble models and prepared PDB structures.
FASTA and JSON files	Sequences and antibody-region annotations.
Graph HDF5 and .pt files	Molecular graphs and ESM sequence embeddings used for scoring.
deeprank_ab.log	Calculation progress, warnings and diagnostic messages; captured diagnostics are also retained for execution failures and timeouts.
provenance.json	Run settings, software and model identity, and input checksums.

Understanding results

Field	Meaning
Model (pdb_id)	Identifier of the scored model.
Predicted DockQ (predicted_dockq)	Predicted complex quality; higher values suggest a better modeled interface. It is a prediction, not DockQ calculated against a reference structure or a binding-affinity measurement.
H-L contact flag (HL_contact_flag)	low_HL_contacts indicates few contacts between the heavy and light chains; ok passes this check; not_applicable means the check does not apply without both chains.
VdW clash flag (vdw_clash_flag)	potential_clash indicates unusual van der Waals interaction energies; ok passes this check.

The flags complement the score and do not establish that a model is experimentally correct. Software details are available in the DeepRank-Ab source documentation.