Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: AntBO: Towards Real-World Automated Antibody Design with Combinatorial
  Bayesian Optimisation   Antibodies are canonically Y-shaped multimeric proteins capable of highly
specific molecular recognition. The CDRH3 region located at the tip of variable
chains of an antibody dominates antigen-binding specificity. Therefore, it is a
priority to design optimal antigen-specific CDRH3 regions to develop
therapeutic antibodies to combat harmful pathogens. However, the combinatorial
nature of CDRH3 sequence space makes it impossible to search for an optimal
binding sequence exhaustively and efficiently, especially not experimentally.
Here, we present AntBO: a Combinatorial Bayesian Optimisation framework
enabling efficient in silico design of the CDRH3 region. Ideally, antibodies
should bind to their target antigen and be free from any harmful outcomes.
Therefore, we introduce the CDRH3 trust region that restricts the search to
sequences with feasible developability scores. To benchmark AntBO, we use the
Absolut! software suite as a black-box oracle because it can score the target
specificity and affinity of designed antibodies in silico in an unconstrained
fashion. The results across 188 antigens demonstrate the benefit of AntBO in
designing CDRH3 regions with diverse biophysical properties. In under 200
protein designs, AntBO can suggest antibody sequences that outperform the best
binding sequence drawn from 6.9 million experimentally obtained CDRH3s and a
commonly used genetic algorithm baseline. Additionally, AntBO finds very-high
affinity CDRH3 sequences in only 38 protein designs whilst requiring no domain
knowledge. We conclude AntBO brings automated antibody design methods closer to
what is practically viable for in vitro experimentation.

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The categories of this paper are: solv-int
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The categories of this paper are: chem-ph
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The categories of this paper are: ao-sci
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The categories of this paper are: hep-ex
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The categories of this paper are: astro-ph
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The categories of this paper are: quant-ph
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The categories of this paper are: adap-org
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The categories of this paper are: bayes-an
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The categories of this paper are: acc-phys
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The categories of this paper are: funct-an
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The categories of this paper are: supr-con
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The categories of this paper are: math
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The categories of this paper are: comp-gas
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The categories of this paper are: cmp-lg
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The categories of this paper are: atom-ph
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The categories of this paper are: q-alg