De Novo H3 prediction by C-terminal kink-biasing (Gray Lab) [here].
Authors introduce an improvement to the prediction of CDR-H3 in the form of a constraint for de-novo decoy generation. Working from the observation that 80% of CDR-H3 have kinked C-Terminal (Weitzner et al., 2015, Structure), they bias the loops to assume this conformation (they prove that it does not force ALL loops to do so!). The constraint is in the form of a pseudo bond angle between Ca for the three C-terminal residues and a pseudo dihedral angle for the three C-terminal residues and one adjacent residue in the framework. The bias takes the form of a penalty score if the generated angle falls outside mean +/- 1s. They use a quite stringent H3 loop benchmark of only 49 loops. Using this constraint on this dataset improves prediction for majority of the loops. They also demonstrate the utility of the score for full Fv homology modeling and Ab-Ag docking.
Therapeutic vs synthetic vs natural antibodies (Ofran Lab) [here].
The authors analyzed 137 Ab-Ag complexes from the PDB. Those from hybridoma and synthetic libraries were classified as ‘Natural’ and those coming from ‘synthetic’ libraries. They demonstrate that synthetic libraries overuse H3 in the number of contacts the antibody forms with the antigen, whereas natural constructs share the paratope with H1& H2 to a larger extent. This, together with their tool, CDRs analyzer (analysis of structural & biochemical properties of ab-ag complex) can be a useful method to inform the design of antibodies.
From the past: TABHU, tools for antibody humanization (Tramontano Lab) [here]. Authors have created a tool to aid antibody humanization. Given a sequence of an antibody, the system would look for the most suitable template from their extensive sequence databases (DIGIT) and germline sequences from IMGT. The templates are assessed on sequence similarity to the query and the similarity of the ‘binding’ mode which is assessed by their paratope prediction tool proABC. After the template had been chosen, the user can produce a structural model of the sequence.