BINDesignER

BINDesignER is the computational protocotol we developed for the optimisation of peptides and for the in-silico maturation of antibody fragments. It is freely available at:

https://github.com/migsoler/BINDesignER

to make it work, you will need to download few other codes, also freely available for academic use:

• GROMACS: http://manual.gromacs.org/documentation/2019.3/download.html
• SCWRL4: http://dunbrack.fccc.edu/svcwrl4/

and a number of scoring functions. The choice of scoring function will depend on your system. For instance, for antibody fragments we  used:

• Irad, Pie*Pisa, Bluues, Haddock, Bach6, FireDock, AutoDock Vina

while for peptides optimisation we simply used AutoDock Vina.