Computer-aided affinity maturation

Computer-aided affinity maturation (CAAM) is a process that uses computational tools to optimize the affinity and specificity of nanobodies through directed evolution.

The CAAM process typically involves the following steps:

Sequence analysis
The amino acid sequence of the nanobody is analyzed to identify potential regions for mutation. This analysis may include identifying amino acid residues that are in contact with the target antigen and regions of the antibody that could be mutated without disrupting the overall structure and function of the antibody.

In silico modeling
Computational tools are used to predict the structural and functional properties of the mutated nanobody. This may involve using molecular dynamics simulations to predict the effects of mutations on the structure and stability of the antibody or using computational docking simulations to predict the binding affinity of the mutated antibody to the target antigen.

Rational design
Based on the sequence analysis and in silico modeling, mutations are designed that are likely to improve the affinity and specificity of the antibody to the target antigen. These mutations may involve changes to amino acid residues that are in contact with the target antigen or changes to the structure of the antibody to improve its binding properties.

The mutated nanobody is validated through experimental methods to ensure that it has the desired binding specificity and affinity to the target antigen and that it has improved stability and reduced immunogenicity.

The mutated nanobody can be further optimized through additional rounds of affinity maturation, using iterative computational modeling and experimental validation.

Overall, CAAM offers a powerful tool for optimizing the affinity and specificity of nanobodies, enabling the creation of high-quality antibodies for a range of applications. Contact us today to learn more about our computer-aided affinity maturation service and how we can support your research needs.