mirror of
https://github.com/HannesStark/boltzgen.git
synced 2026-06-04 11:54:23 +08:00
184 lines
3.7 KiB
YAML
184 lines
3.7 KiB
YAML
entities:
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- protein:
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id: G
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sequence: 15..20AAAAAAVTTTT18PPP # range between 15 and 20 inclusive on both sides
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- protein:
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id: R
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sequence: 3..5C6C3 # Random number of design residues between 3 and 5, then a Cystein, then 6 design residues, then ...
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- ligand:
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id: Q
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ccd: WHL
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- protein:
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id: H
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sequence: 17
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secondary_structure: # No secondary structure specified, defaults
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- file:
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path: 7rpz.cif
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include:
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- chain:
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id: A
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- chain:
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id: B
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include_proximity:
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- chain:
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id: A
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res_index: 10..16
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radius: 35
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binding_types:
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- chain:
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id: A
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binding: 5..7,13
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- chain:
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id: B
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not_binding: "all"
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structure_groups:
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- group:
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visibility: 1
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id: A
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res_index: 10..16
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- group:
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visibility: 2
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id: B
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- group:
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visibility: 0
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id: A
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res_index: 13
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design:
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- chain:
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id: A
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res_index: ..4,20..27
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secondary_structure:
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- chain:
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id: A
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loop: 1
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helix: 2..3
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sheet: 4
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design_insertions:
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- insertion:
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id: A
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res_index: 20 # The 20th residue will be a designed one (starting to count from 1)
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num_residues: 2..9
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secondary_structure: HELIX # One of UNSPECIFIED (default), LOOP, HELIX, SHEET.
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- protein:
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id: A
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sequence: AAAAAAAAAAAAAAAAAAAAAAAA
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binding_types: uuuuBBBuNNNuBuu # the missing specifications will be 'u' by default
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- file:
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path: 7rpz.cif
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fuse: A
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include:
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- chain:
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id: A
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res_index: ..5
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- protein:
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id: B
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sequence: AAAAAAAAAAAAAAAAAAAAAAAA
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binding_types:
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binding: 5..7,13
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not_binding: 9..11
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- ligand:
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id: [C, D]
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ccd: SAH
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- ligand:
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id: [E, F]
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smiles: 'N[C@@H](Cc1ccc(O)cc1)C(=O)O'
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binding_types: B
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- file:
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path: 7rpz.cif
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include: "all"
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exclude:
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- chain:
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id: A
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res_index: ..5
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structure_groups:
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- group:
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visibility: 1
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id: "all"
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- group:
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visibility: 0
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id: A
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res_index: 10..16
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- file:
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path: 8r3a.cif
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include:
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- chain:
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id: A
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- chain:
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id: B
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binding_types:
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- chain:
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id: A
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binding: 5..7,13
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- chain:
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id: B
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not_binding: "all"
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structure_groups:
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- group:
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visibility: 1
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id: A
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res_index: 10..13
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- group:
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visibility: 2
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id: B
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- group:
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visibility: 0
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id: A
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res_index: 13
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design:
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- chain:
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id: A
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res_index: 14..19
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secondary_structure:
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- chain:
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id: A
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loop: 14
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helix: 15..17
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sheet: 19
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- protein:
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id: S
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sequence: 10C6C3
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- protein:
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id: T
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sequence: C10C6C3C
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cyclic: true
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constraints:
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# specify connections as if the minimum possible number of residues was sampled
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- bond:
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atom1: [R, 4, SG] # connection for a helicon
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atom2: [Q, 1, CK]
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- bond:
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atom1: [R, 11, SG]
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atom2: [Q, 1, CH]
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- bond:
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atom1: [S, 11, SG] # connection for a disulfide bond
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atom2: [S, 18, SG]
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- bond:
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atom1: [T, 12, SG]
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atom2: [T, 19, SG]
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- total_len:
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min: 10
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max: 20 |