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Fast immune receptor protein structure prediction

ImmuneBuilder is a collection of tools for predicting structures of Nanobodies (NanoBodyBuilder2), Antibodies (ABodyBuilder2), and T-Cell receptors (TCRBuilder2). It cannot incorporate the antigen into the structure prediction, for example it would predict the structure of the ScFv or VHH without a target present. It is much faster than comparable models like AlphaFold, while maintaining state of the art accuracy.

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Methods

Immunebuilder is a modified version of AlphaFold-Multimer specialized for antibodies. It treats residues as rigid bodies rather than flexible, defined by their position and orientation only.

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Benchmarking

On a benchmark of 34 recently solved antibodies, ABodyBuilder2 predicts CDR-H3 loops with an RMSD of 2.81Å, a 0.09Å improvement over AlphaFold-Multimer, while being over a hundred times faster. Similar results are also achieved for nanobodies, where it predicts CDR-H3 loops with an average RMSD of 2.89Å, a 0.55Å improvement over AlphaFold2, and TCRs. ImmuneBuilder also gives an error estimate for every residue in its final prediction.

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