CycleDesigner is a novol workflow for de novo cyclic peptide design. The modified powerful RFdiffusion model(CycRFdiffusion) allows the generation of cyclic peptide backbone and integrated it with ProteinMPNN and HighFold to design binders for specific targets.
You can install the RFdiffusion at first, and then copy the source codes of CycleDesigner into the installed RFdifusion preject.
To run the generation, type
./rfd_zch_inference.sh /YOUR/PDB/PATH/pdb.pdb
The inference adapt for the targets with binders only, if there is no binders in pdb file, please type follows to run the generation.
./scripts/run_inference.py 'contigmap.contigs=[A1-n/0 a-a]' 'ppi.hotspot_res=[A1,A2]' inference.deterministic=Ture inference.num_designs=5 inference.model_directory_path=/YOUR/MODEL/PATH inference.input_pdb=/YOUR/PDB/PATH/pdb.pdb inference.output_prefix=/YOUR/OUTPUT/CYCPEP/NAME > /PATH/NAME.log 2>&1
The output trajectory files of molecular dynamics simulation prosess have uploaded at Zenodo.