prescient-ibex 0.1.1

Lightweight antibody structure prediction tool

Ibex 🐐

Ibex is a lightweight antibody and TCR structure prediction model.

Installation

Ibex can be installed through pip with

pip install prescient-ibex

Alternatively, you can use uv and create a new virtual environment

uv venv --python 3.10
source .venv/bin/activate
uv pip install -e .

Usage

The simplest way to run inference is through the ibex command, e.g.

ibex --fv-heavy EVQLVESGGGLVQPGGSLRLSCAASGFNIKDTYIHWVRQAPGKGLEWVARIYPTNGYTRYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSRWGGDGFYAMDYWGQGTLVTVSS --fv-light DIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIK --output prediction.pdb

You can provide a csv (with the --csv argument) or a parquet file (with the --parquet argument) and run a batched inference writing the output into a specified directory with

ibex --csv sequences.csv --output predictions

where sequences.csv should contain a fv_heavy and fv_light column with heavy and light chain sequences, and optionally an id column with a string that will be used as part of the output PDB filenames.

By default, structures are predicted in the holo conformation. To predict the apo state, use the --apo flag.

To run a refinement step on the predicted structures, use the --refine option. Additional checks to fix cis-isomers and D-stereoisomers during refinement can be activated with --refine-checks.

Instead of running Ibex, you can use --abodybuilder3 to run inference with the ABodyBuilder3 model.

To run Ibex programmatically, you can use

from ibex import Ibex, checkpoint_path, inference
ckpt = checkpoint_path("ibex")
ibex_model = Ibex.load_from_ensemble_checkpoint(ckpt)
inference(ibex_model, fv_heavy, fv_light, "prediction.pdb")

to predict structures for multiple sequence pairs, batch_inference is recommended instead of inference.

Predictions on nanobodies and TCRs

To predict nanobody structures, leave out the fv_light argument, or set it as "" or None in the csv column.

For inference on TCRs, you should provide the variable beta chain sequence as fv_heavy and the alpha chain as fv_light. Ibex has not been trained on gamma and delta chains.

License

The codebase and the ABodyBuilder3 model weights are available under Apache 2.0 license.

The model weights for Ibex are available under Genentech Apache 2.0 Non-Commercial license.

Ibex uses as input representation embeddings from ESMC 300M, which is licensed under the EvolutionaryScale Cambrian Open License Agreement.

Citation

If this code is useful to you please cite our paper using the following bibtex entry,

@article{ibex,
    author = {Dreyer et al.},
    title = "{Conformation-Aware Structure Prediction of Antigen-Recognizing Immune Proteins}",
    year = {2025},
}