Files

Files:
Machine learning:

1. Jupyter notebook for data exploration, training and validation: Paper_nanobodies_design.ipynb;
2. Data set: ifa.txt, ifa.csv (where ifa corresponds to the output of Rosetta's interface analyzer);

Rosetta design:

1. ifa.xml: script to run the Rosetta InterfaceAnalyzer protocol;
2. design.xml: script to design the Nanobody;

Molecular dynamics:
1. md.mdp: simulation production parameters
2. plumed.dat: metadynamics run file
3. topol.top: topology file
4. toppar: topology parameters
5. step3_input.gro: initial coordinates for the PDB ID 6W41 with glycans

Docking:
1. complex.pdb: structure design via Rosetta;
2. af3.pdb: structure predict with AF3;
3. cluspro.pdb: structure predict with ClusPro;