Our paper “A consensus protocol for the in silico optimisation of antibody fragments” has just been accepted for publications, marking the first milestone of our AIRC project “Computational design of customised nanobodies for oncology applications: prognostic candidates for HER2 as first case”.

In this paper we present BINDesignER: our in silico mutagenetic protocol for the computational optimisation of single domain antibodies (or nanobodies, VHHs). We show in this paper that, by aplying our optimisation algorithm, we could obtain a VHH mutant with significantly enhanced experimental affinity with respect to the original VHH it matured from. The protocol can be employed as it is for the optimization of peptides, antibody fragments, and (given enough computational power) of larger antibodies.