Structure conditioned hallucinated CDR sequences

Datasets accompanying publication https://doi.org/10.1101/2022.06.06.494991 (Published in Frontiers in Immunology). Please refer to the final version of the manuscript on Frontiers.

RAbD dataset (Figure 2 in preprint/publication): Structure conditioned hallucinated sequences for all 6 CDR loops of 60 antibodies (see publication above for more details) with wildtype seeding (runs_wtseed) and without wildtype seeding (runs_noseed). Full sequences are under runs_<>/<benchamark_name>/<cdr>/results/sequences.fasta.

DeepAb Testset (SI Table 1, SI Figure 4 in preprint/publication): Structure conditioned hallucinated sequences for all 6 CDR loops of 20 antibodies selected from the DeepAb test set (see publication above for more details) with wildtype seeding (runs_wtseed) and without wildtype seeding (runs_noseed). Full sequences are under runs_<>/<benchamark_name>/<cdr>/results/sequences.fasta.

Trastuzumab hallucination in various modes described in the manuscript.

1. Unrestricted hallucination: In "unrestricted.tar". Contains hallucination results in the folder "results". Forward folded structures and metrics in "forward_folding", results of virtual screening in "virtual_binding", results of filtering for both folding and virtual screening in "results_filtered_output", and the results from comparison of multiple folding methods (DeepAb and IgFold) in "results_folding_methods".

2. Motif-restricted hallucination (positions 95, 100A on heavy chain): In "res2pos_95and100A.tar". Contains hallucination results in the folder "results". Forward folded structures and metrics in "forward_folding", results of virtual screening in "virtual_binding", results of filtering for both folding and virtual screening in "results_filtered_output", and the results from comparison of multiple folding methods (DeepAb and IgFold) in "results_folding_methods".

3. Motif-restricted hallucination (positions 99, 100A on heavy chain): In "res2pos_99and100A.tar". Contains hallucination results in the folder "results". Forward folded structures and metrics in "forward_folding", results of virtual screening in "virtual_binding", results of filtering for both folding and virtual screening in "results_filtered_output", and the results from comparison of multiple folding methods (DeepAb and IgFold) in "results_folding_methods".

4. Motif-restricted hallucination (positions 95, 99, 100, 100A on heavy chain): In "res4pos.tar". Contains hallucination results in the folder "results". Forward folded structures and metrics in "forward_folding", results of virtual screening in "virtual_binding", results of filtering for both folding and virtual screening in "results_filtered_output", and the results from comparison of multiple folding methods (DeepAb and IgFold) in "results_folding_methods".

5. Motif-restricted (positions 99, 100A on heavy chain) and sequence-restricted (restricted to wildtype sequence) hallucination: In "res2pos_95and100A_and_sequence.tar". Contains hallucination results in the folder "results". Forward folded structures and metrics in "forward_folding", results of virtual screening in "virtual_binding", results of filtering for both folding and virtual screening in "results_filtered_output", and the results from comparison of multiple folding methods (DeepAb and IgFold) in "results_folding_methods".

For reproducing data, refer to code and methods in the preprint/published version.