Article
A consensus protocol for the in silico optimisation of antibody fragments.
Chemical communications (Cambridge, England) - 19 Nov 2019
Soler Miguel A, Medagli Barbara, Semrau Marta S, Storici Paola, Bajc Gregor, de Marco Ario, Laio Alessandro, Fortuna Sara
Abstract excerpt
We present an in silico mutagenetic protocol for improving the binding affinity of single domain antibodies (or nanobodies, VHHs). The method iteratively attempts random mutations in the interacting region of the protein and evaluates the resulting binding affinity towards the target by scoring, with a collection of scoring functions, short explicit solvent molecular dynamics trajectories of the binder-target...
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