| entities: | |
| - protein: | |
| id: G | |
| sequence: 15..20AAAAAAVTTTT18PPP # range between 15 and 20 inclusive on both sides | |
| residue_constraints: | |
| - position: 1 | |
| allowed: A # Only Alanine at position 1 | |
| - position: 3..5 | |
| disallowed: CM # No Cysteine or Methionine at positions 3-5 | |
| - position: 8 | |
| allowed: AGS # Only Ala, Gly, or Ser at position 8 | |
| - protein: | |
| id: R | |
| sequence: 3..5C6C3 # Random number of design residues between 3 and 5, then a Cystein, then 6 design residues, then ... | |
| - ligand: | |
| id: Q | |
| ccd: WHL | |
| - protein: | |
| id: H | |
| sequence: 17 | |
| secondary_structure: # No secondary structure specified, defaults | |
| - file: | |
| path: 7rpz.cif | |
| include: | |
| - chain: | |
| id: A | |
| - chain: | |
| id: B | |
| include_proximity: | |
| - chain: | |
| id: A | |
| res_index: 10..16 | |
| radius: 35 | |
| binding_types: | |
| - chain: | |
| id: A | |
| binding: 5..7,13 | |
| - chain: | |
| id: B | |
| not_binding: "all" | |
| structure_groups: | |
| - group: | |
| visibility: 1 | |
| id: A | |
| res_index: 10..16 | |
| - group: | |
| visibility: 2 | |
| id: B | |
| - group: | |
| visibility: 0 | |
| id: A | |
| res_index: 13 | |
| design: | |
| - chain: | |
| id: A | |
| res_index: ..4,20..27 | |
| secondary_structure: | |
| - chain: | |
| id: A | |
| loop: 1 | |
| helix: 2..3 | |
| sheet: 4 | |
| design_insertions: | |
| - insertion: | |
| id: A | |
| res_index: 20 # The 20th residue will be a designed one (starting to count from 1) | |
| num_residues: 2..9 | |
| secondary_structure: HELIX # One of UNSPECIFIED (default), LOOP, HELIX, SHEET. | |
| - protein: | |
| id: A | |
| sequence: AAAAAAAAAAAAAAAAAAAAAAAA | |
| binding_types: uuuuBBBuNNNuBuu # the missing specifications will be 'u' by default | |
| - file: | |
| path: 7rpz.cif | |
| fuse: A | |
| include: | |
| - chain: | |
| id: A | |
| res_index: ..5 | |
| - protein: | |
| id: B | |
| sequence: AAAAAAAAAAAAAAAAAAAAAAAA | |
| binding_types: | |
| binding: 5..7,13 | |
| not_binding: 9..11 | |
| - ligand: | |
| id: [C, D] | |
| ccd: SAH | |
| - ligand: | |
| id: [E, F] | |
| smiles: 'N[C@@H](Cc1ccc(O)cc1)C(=O)O' | |
| binding_types: B | |
| - file: | |
| path: 7rpz.cif | |
| include: "all" | |
| exclude: | |
| - chain: | |
| id: A | |
| res_index: ..5 | |
| structure_groups: | |
| - group: | |
| visibility: 1 | |
| id: "all" | |
| - group: | |
| visibility: 0 | |
| id: A | |
| res_index: 10..16 | |
| - file: | |
| path: 8r3a.cif | |
| include: | |
| - chain: | |
| id: A | |
| - chain: | |
| id: B | |
| binding_types: | |
| - chain: | |
| id: A | |
| binding: 5..7,13 | |
| - chain: | |
| id: B | |
| not_binding: "all" | |
| structure_groups: | |
| - group: | |
| visibility: 1 | |
| id: A | |
| res_index: 10..13 | |
| - group: | |
| visibility: 2 | |
| id: B | |
| - group: | |
| visibility: 0 | |
| id: A | |
| res_index: 13 | |
| design: | |
| - chain: | |
| id: A | |
| res_index: 14..19 | |
| secondary_structure: | |
| - chain: | |
| id: A | |
| loop: 14 | |
| helix: 15..17 | |
| sheet: 19 | |
| - protein: | |
| id: S | |
| sequence: 10C6C3 | |
| - protein: | |
| id: T | |
| sequence: C10C6C3C | |
| cyclic: true | |
| constraints: | |
| # specify connections as if the minimum possible number of residues was sampled | |
| - bond: | |
| atom1: [R, 4, SG] # connection for a helical peptides with WHL staple | |
| atom2: [Q, 1, CK] | |
| - bond: | |
| atom1: [R, 11, SG] | |
| atom2: [Q, 1, CH] | |
| - bond: | |
| atom1: [S, 11, SG] # connection for a disulfide bond | |
| atom2: [S, 18, SG] | |
| - bond: | |
| atom1: [T, 12, SG] | |
| atom2: [T, 19, SG] | |
| - total_len: | |
| min: 10 | |
| max: 20 |