input_specs.yaml

                sequences:
            
                      - protein:
                
                        id: B
                
                        sequence: 8..18
                
                        cyclic: true
                
                      - file:
                
                        path: 1mk5.cif (Streptavidin)
                
                        structure_groups:
                
                          # Fix structure
                
                          - group:
                
                            id: A
                
                            visibility: 1
                
                          # Make loop flexible
                
                              - group:
                    
                                id: A
                    
                                visibility:
                        0
                    
                                res_index:
                        32..42
                    
                Click highlighted lines to toggle constraints

Design Specification Language (DSL): This YAML configuration controls the generation. Here, we request a cyclic peptide binder (yellow) for the Streptavidin target (blue). We explicitly mark a loop on the target as flexible (orange), allowing the model to adjust it for better binding.