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. 2022 Oct 21;13:999034. doi: 10.3389/fimmu.2022.999034

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Copyright © 2022 Mahajan, Ruffolo, Frick and Gray

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Strategies for guiding hallucination to relevant sequence spaces. (A) Restricted hallucination allows restricting hallucination to relevant sequence spaces for specific design objectives such as sampling close to the wildtype sequence or retaining motifs for binding. (B) Guiding hallucination towards different sequence spaces via geometric losses (L_G , unrestricted hallucination), geometric and motif loss (L_M , motif restricted hallucination), and geometric and sequence loss (L_S , sequence restricted hallucination). (C) Trastuzumab binders dataset (TBS) from Mason et al. (47) screening of single-site and combinatorial libraries for expression and binding. (D) Hallucinated sequences shown as sequence logos for 3 modes of hallucination for the CDR H3 loop of Trastuzumab. (E) Comparison of LDs of hallucinated sequences with different strategies with experimentally identified binders from the TBS dataset.