Structure conditioned hallucinated CDR sequences

<p><em><strong>Datasets accompanying publication&nbsp;https://doi.org/10.1101/2022.06.06.494991</strong></em> (Published in Frontiers in Immunology). Please refer to the final version of the manuscript on Frontiers.</p> <p><strong>RAbD dataset (Figure 2 in preprint/publication)</strong>: Structure conditioned hallucinated sequences for all 6 CDR loops of&nbsp;60 antibodies (see publication above for more details) with wildtype seeding (runs_wtseed) and without wildtype seeding (runs_noseed). Full sequences are under runs_&lt;&gt;/&lt;benchamark_name&gt;/&lt;cdr&gt;/results/sequences.fasta.</p> <p><strong>DeepAb Testset (SI Table 1, SI Figure 4 in preprint/publication)</strong>: 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_&lt;&gt;/&lt;benchamark_name&gt;/&lt;cdr&gt;/results/sequences.fasta.</p> <p><strong>Trastuzumab hallucination in various modes described in the manuscript.</strong></p> <p>1. <strong>Unrestricted hallucination</strong>: In <strong>&quot;unrestricted.tar&quot;</strong>. Contains hallucination results in the folder &quot;results&quot;. Forward folded structures and metrics in &quot;forward_folding&quot;, results of virtual screening in &quot;virtual_binding&quot;, results of filtering for both folding and virtual screening in &quot;results_filtered_output&quot;, and the results from comparison of multiple folding methods (DeepAb and IgFold) in &quot;results_folding_methods&quot;.</p> <p>2.&nbsp;<strong>Motif-restricted&nbsp;hallucination (positions 95, 100A on heavy chain)</strong>: In &quot;<strong>res2pos_95and100A.tar&quot;</strong>. Contains hallucination results in the folder &quot;results&quot;. Forward folded structures and metrics in &quot;forward_folding&quot;, results of virtual screening in &quot;virtual_binding&quot;, results of filtering for both folding and virtual screening in &quot;results_filtered_output&quot;, and the results from comparison of multiple folding methods (DeepAb and IgFold) in &quot;results_folding_methods&quot;.</p> <p>3.&nbsp;<strong>Motif-restricted&nbsp;hallucination (positions 99, 100A on heavy chain)</strong>: In &quot;<strong>res2pos_99and100A.tar</strong>&quot;. Contains hallucination results in the folder &quot;results&quot;. Forward folded structures and metrics in &quot;forward_folding&quot;, results of virtual screening in &quot;virtual_binding&quot;, results of filtering for both folding and virtual screening in &quot;results_filtered_output&quot;, and the results from comparison of multiple folding methods (DeepAb and IgFold) in &quot;results_folding_methods&quot;.</p> <p>4.&nbsp;<strong>Motif-restricted&nbsp;hallucination (positions 95, 99, 100, 100A on heavy chain)</strong>: In &quot;<strong>res4pos.tar</strong>&quot;. Contains hallucination results in the folder &quot;results&quot;. Forward folded structures and metrics in &quot;forward_folding&quot;, results of virtual screening in &quot;virtual_binding&quot;, results of filtering for both folding and virtual screening in &quot;results_filtered_output&quot;, and the results from comparison of multiple folding methods (DeepAb and IgFold) in &quot;results_folding_methods&quot;.</p> <p>5.&nbsp;<strong>Motif-restricted&nbsp;(positions 99, 100A on heavy chain) and sequence-restricted (restricted to wildtype sequence) hallucination</strong>: In &quot;<strong>res2pos_95and100A_and_sequence.tar</strong>&quot;. Contains hallucination results in the folder &quot;results&quot;. Forward folded structures and metrics in &quot;forward_folding&quot;, results of virtual screening in &quot;virtual_binding&quot;, results of filtering for both folding and virtual screening in &quot;results_filtered_output&quot;, and the results from comparison of multiple folding methods (DeepAb and IgFold) in &quot;results_folding_methods&quot;.</p> <p>For reproducing data, refer to code and methods in the preprint/published version.</p>