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**IMPORTANT:** ⚠️ All residue indices are specified **starting at 1** and we use the canonical mmcif residue index `label_asym_id`, and **not** the `auth_asym_id` author residue index!
You can check the indexing in your mmcif file by opening it in https://molstar.org/viewer/, hovering over a residue, and checking the index on the bottom right. You will see something like this where **41 is the index we use, the auth id 22 is incorrect**:
After you constructed your `.yaml` file we recommend that you run the `check` command on it:
1. Run `boltzgen check example/vanilla_peptide_with_target_binding_site/beetletert.yaml`.
2. Visualize the resulting mmcif file in a protein structure viewer (e.g. PyMOL, Chimera, or online: https://molstar.org/viewer/).
3. Your viewer should show the binding site in a different color than the rest of the target.
# Example based explanation:
We provide many example `.yaml` files in the `example/` directory, including:
- [design_spec_showcasing_all_functionalities.yaml](design_spec_showcasing_all_functionalities.yaml)
- [vanilla_peptide_with_target_binding_site/beetletert.yaml](vanilla_peptide_with_target_binding_site/beetletert.yaml)
- [peptide_against_specific_site_on_ragc/rragc.yaml](peptide_against_specific_site_on_ragc/rragc.yaml)
- [nanobody/penguinpox.yaml](nanobody/penguinpox.yaml)
- [fab_targets/pdl1.yaml](fab_targets/pdl1.yaml)
- [denovo_zinc_finger_against_dna/zinc_finger.yaml](denovo_zinc_finger_against_dna/zinc_finger.yaml)
- [protein_binding_small_molecule/chorismite.yaml](protein_binding_small_molecule/chorismite.yaml)
- [small_molecule_from_file_and_smiles/4g37.yaml](small_molecule_from_file_and_smiles/4g37.yaml)
Small example of a protein design against a target protein without binding site specified:
```yaml
entities:
# Designed protein with between 80 and 140 residues
# (The length is randomly sampled)
- protein:
id: B
sequence: 80..140
# The target is extracted from a .cif file
- file:
path: hard_targets/6m1u.cif
# Which chain in the .cif file to use as target (uses all chains if unspecified)
include:
- chain:
id: A
```
**IMPORTANT:** ⚠️ File references inside a yaml file (e.g. to cif files) are interpreted relative to the directory of the yaml file.
Example highlighting many (not all) functionalities:
```yaml
entities:
# Specification of the target which is extracted from a .cif file
- file:
path: 8r3a.cif
# Which chain and residues in the .cif file to use as target (uses all chains if unspecified)
include:
- chain:
id: A
res_index: 2..50,55.. # residues between 2 and 50 and anything larger than 55
- chain:
id: B
# Which regions of the target the design should or should NOT
# bind to (this can be left unspecified, then we just bind anywhere)
binding_types:
- chain:
id: A
binding: 5..7,13
- chain:
id: B
not_binding: "all"
# Which regions of the target should have their structure specified.
# By default, everything is visibility 1 which means that the structure is specified.
# If the visibility is 0, then the structure is not specified.
structure_groups:
- group:
visibility: 1
id: A
res_index: 10..13
- group:
# The relative positioning of things in structure group 2
# is not specified w.r.t to things in structure group 1
visibility: 2
id: B
# Overwrite the previous visibility setting and set it to 0 for res_index 13
- group:
visibility: 0
id: A
res_index: 13
# Optionally you can say that some residues in a loaded .cif file should also be redesigned.
design:
- chain:
id: A
res_index: 14..19
# For designed regions you can say what secondary structure they should have
secondary_structure:
- chain:
id: A
loop: 14
helix: 15..17
sheet: 19
# Specify a NON-designed protein chain
- protein:
id: X
sequence: AAVTTTTPPP
# Specify a designed protein chain
# Numbers specify what is being designed
- protein:
id: G
# random number between 15 and 20 of designed residues (inclusive)
sequence: 15..20AAAAAAVTTTT18PPP
# A designed helical peptides with WHL staple
# (see the constraints below that connect the peptide with the WHL ligand)
- protein:
id: R
# Random number of design residues between 3 and 5,
# then a Cysteine, then 6 design residues, then ...
sequence: 3..5C6C3
- ligand:
id: Q
ccd: WHL
# A designed peptide with 17 residues
- protein:
id: H
sequence: 17
# specification for a designed peptide with two Cys and a disulfide bond (see constraints)
- protein:
id: S
sequence: 10..14C6C3
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 between small molecule and designed peptide
atom2: [Q, 1, CK]
- bond:
atom1: [R, 11, SG] # connection for a helical peptides with WHL staple between small molecule and designed peptide
atom2: [Q, 1, CH]
- bond:
atom1: [S, 11, SG] # connection for a disulfide bond between Cys and Cys in designed peptide
atom2: [S, 18, SG]
```
# Detailed Explanation
```yaml
entities:
# Define proteins, ligands, and structure files
- protein: ...
- ligand: ...
- file: ...
constraints:
# Define bonds and total length constraints
- bond: ...
- total_len: ...
```
### Entities Section
The `entities` section defines all the components of your design:
#### Protein Sequences
Define custom protein sequences with design flexibility:
```yaml
entities:
- protein:
id: G # Unique identifier
sequence: 15..20AAAAAAVTTTT18PPP # Mix of fixed residues and design regions
binding_types: uuuuBBBuNNNuBuu # Binding specifications (optional)
secondary_structure: HHHLLLEEE # Secondary structure constraints for designed regions (optional)
```
**Sequence notation:**
- `15..20` - Design between 15-20 residues (inclusive)
- `AAAA` - Fixed amino acid sequence
- `18` - Design exactly 18 residues
- `3..5C6C3` - Variable design residues, then fixed Cys, then more design
**Binding types:**
- `B` - Binding residue
- `N` - Non-binding residue
- `u` - Unspecified (default)
- Can specify as string: `uuuuBBBuNNNuBuu`
- Or as ranges:
```yaml
binding_types:
binding: 5..7,13 # Residues 5-7 and 13 are binding
not_binding: 9..11 # Residues 9-11 are non-binding
```
#### Ligands
Define small molecule ligands using CCD codes or SMILES:
```yaml
# Using Chemical Component Dictionary (CCD) code
entities:
- ligand:
id: [E, F] # specify list of IDs to copy the entity
ccd: WHL
binding_types: B
# Using SMILES string
entities:
- ligand:
id: Q
smiles: 'N[C@@H](Cc1ccc(O)cc1)C(=O)O'
binding_types: B
```
#### Structure Files
Include existing protein structures from PDB/mmCIF files:
```yaml
entities:
- file:
path: 7rpz.cif
# Include specific chains
include:
- chain:
id: A
- chain:
id: B
# Include by proximity
include_proximity:
- chain:
id: A
res_index: 10..16
radius: 35
# Exclude specific regions
exclude:
- chain:
id: A
res_index: ..5 # Exclude residues 1-5
# Reset residue numbering
reset_res_index:
- chain:
id: A
```
# Advanced Options
**Design regions:** Specify which residues to redesign
```yaml
entities:
...
- file:
...
design:
- chain:
id: A
res_index: ..4,20..27 # Redesign residues 1-4 and 20-27
```
**Secondary structure constraints:**
```yaml
entities:
...
- protein:
...
secondary_structure:
- chain:
id: A
loop: 1 # Residue 1 should be loop
helix: 2..3 # Residues 2-3 should be helix
sheet: 4 # Residue 4 should be sheet
```
**Structure visibility groups:**
```yaml
entities:
...
- file:
...
structure_groups:
- group:
visibility: 1 # Visibility level (0=hidden, 1=visible, 2=highlighted)
id: A
res_index: 10..16
```
**Design insertions:**
```yaml
entities:
...
- file:
...
design_insertions:
- insertion:
id: A
res_index: 20 # Insert after residue 20
num_residues: 2..9 # Insert 2-9 residues
secondary_structure: HELIX # UNSPECIFIED, LOOP, HELIX, or SHEET
```
**Binding type specifications:**
```yaml
entities:
...
- protein:
...
binding_types:
- chain:
id: A
binding: 5..7,13
- chain:
id: B
not_binding: "all"
```
### Constraints Section
Define structural constraints between components:
#### Bond Constraints
Create covalent bonds between specific atoms:
```yaml
constraints:
- bond:
atom1: [R, 4, SG] # [chain_id, residue_number, atom_name]
atom2: [Q, 1, CK] # Connect sulfur of Cys-4 in chain R to atom CK in ligand Q
```
We now support constraints specifications of small molecules from the input file and from smiles. Check `examples/small_molecule_from_file_and_smiles/4g37.yaml`. Below is brief guidelines:
* Small molecules from the file: check `atom_name` from the CCD and specify it.
* Small molecules from the smiles: count index of target element from the smiles and specify its element type with index (e.g. C6, for 6th carbon from the smiles).
Here is a comprehensive list of all the keys from your YAML file with explanations for each.
***
### Top-Level Keys
* `entities`: The main list containing all molecular components of the system, such as proteins, ligands, or imported files.
* `constraints`: A list of rules or conditions to apply to the system, like specific bonds between entities or total length restrictions.
---
### Entity Types (Keys within the `entities` list)
* `protein`: Defines a protein entity.
* `ligand`: Defines a small molecule ligand.
* `file`: Specifies an external structure file (e.g., a `.cif` file) to import parts of the system from.
---
### Keys for `protein` Entities
* `id`: A unique identifier for the protein chain (e.g., 'A', 'G').
* `sequence`: Defines the amino acid sequence of the protein. This can include numbers to specify lengths of residues to be designed.
* `secondary_structure`: Specifies the secondary structure of the protein.
* `binding_types`: Defines which residues are involved in binding. Can be a string or a more detailed dictionary.
* `cyclic`: A boolean (`true` or `false`) indicating if the protein is cyclic.
---
### Keys for `ligand` Entities
* `id`: A unique identifier for the ligand. Can be a single ID or a list of IDs.
* `ccd`: The Chemical Component Dictionary ID for the ligand (e.g., 'SAH').
* `smiles`: The SMILES string representing the ligand's chemical structure.
* `binding_types`: Specifies binding information, often a simple character like 'B' for binding.
---
### Keys for `file` Entities
* `path`: The file path to the structure file to be included (e.g., 'example/7rpz.cif').
* `msa`: A global flag for Multiple Sequence Alignment for the chains in the file. Can be overwritten by individual chain settings.
* `include`: Specifies which parts of the file to include. Can be the string `"all"` or a list of chains.
* `exclude`: Specifies which parts of an included file to exclude.
* `fuse`: Specifies a chain to which subsequent protein entities will be fused.
* `include_proximity`: Includes residues from the file that are within a certain distance of a specified chain.
* `binding_types`: Defines binding interactions for specific chains within the file.
* `structure_groups`: Defines groups of residues for visualization or other purposes.
* `design`: Specifies which residues in the included chains are designable.
* `secondary_structure`: Defines the secondary structure for specific residues within included chains.
* `design_insertions`: Specifies where to insert new designable residues.
---
### Keys for `constraints`
* `bond`: Defines a covalent bond to be formed between two specified atoms in the system.
* `atom1`: The first atom in the bond.
* `atom2`: The second atom in the bond.
* `total_len`: Constrains the total length of the polymeric system.
* `min`: The minimum allowed total length.
* `max`: The maximum allowed total length.
---
### Nested Keys (found within multiple entity types)
* `chain`: A sub-dictionary used in `include`, `exclude`, `binding_types`, `design`, and `secondary_structure` to specify a particular protein chain.
* `id`: The identifier of the chain.
* `msa`: A specific MSA setting for this chain, overriding the global `msa` flag.
* `res_index`: Specifies a range or list of residue indices.
* `radius`: Used in `include_proximity` to define a distance in Angstroms.
* `binding`: Specifies residues that are part of a binding site.
* `not_binding`: Specifies residues that are not part of a binding site.
* `loop`, `helix`, `sheet`: Used in `secondary_structure` to define the structure of specific residues.
* `group`: Used in `structure_groups` to define a residue group.
* `id`: The identifier of the chain or `"all"`.
* `visibility`: A numerical value to control how the group is displayed.
* `res_index`: The residues included in this group.
* `insertion`: Used in `design_insertions`.
* `id`: The chain ID where the insertion occurs.
* `res_index`: The residue index after which the insertion is made.
* `num_residues`: The number or range of residues to be inserted.
* `secondary_structure`: The desired secondary structure for the inserted residues (e.g., `HELIX`). |