The new phage display technologies have revolutionized the antibody field by allowing the creation of libraries containing antibody fragments as scFv, Fab or nanobodies. The microbial expression systems enable easy and cheap production of specific antibody fragments and efficient protein engineering.

But, the use of antibodies or fragments as therapeutics requires optimizing several of their key parameters as binding affinity, pharmacokinetics or folding stability.

Addressing these challenges requires the use of a suitable computational tool, a combination of elements that produce value in the understanding of antigenic interactions. One of these components is performing numbering for rational analyses.

Scaligner ensures that all antibody sequences are numbered in a universally-recognized way

Scaligner is a platform for automatically analyzing, displaying and storing antibody sequences in a secure and long-term repository.

First, each antibody chain is assigned the most similar germline, based on the nucleotide or amino acid sequence. Germlines identification is based on a user-modifiable germline database that allows grouping germlines in species or project-dependent sets.

Then, complementarity determining regions (CDRs) and framework regions are defined according to the numbering scheme.

Finally, amino acids are numbered to be compared and to identify equivalent positions. Mutations from germline, potential post-translational modification site are also listed.

The sequences can be annotated using the most popular numbering schemes Kabat or IMGT systems.

The process for identifying regions can be applied both to nucleotide and amino acid sequences and to any type of scaffolds (germlines or proteins scaffolds). Scaligner will for instance identify CDRs and framework regions in ScFv sequences.

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