Protein Binder Design
Protein binder design workflow - generate protein binders.
BinderScores
dataclass
BinderScores(iptm: float | None = None, design_ptm: float | None = None, quality_score: float | None = None, bb_rmsd: float | None = None, loop: float | None = None, helix: float | None = None, sheet: float | None = None, liability_score: float | None = None, liability_num_violations: int | None = None, liability_high_severity_violations: int | None = None, min_interaction_pae: float | None = None, delta_sasa_refolded: float | None = None, plip_hbonds_refolded: int | None = None, plip_saltbridge_refolded: int | None = None, num_tokens: int | None = None, design_hydrophobicity: float | None = None, num_filters_passed: int | None = None)
Scores for a generated protein binder design.
Attributes:
| Name | Type | Description |
|---|---|---|
iptm |
float | None
|
interface predicted TM-score (0-1, higher is better) |
design_ptm |
float | None
|
predicted TM-score for the designed binder (0-1) |
quality_score |
float | None
|
overall quality score (0-1, higher is better) |
bb_rmsd |
float | None
|
backbone RMSD compared to initial structure (Angstrom) |
loop |
float | None
|
fraction of residues in loop conformation |
helix |
float | None
|
fraction of residues in helix conformation |
sheet |
float | None
|
fraction of residues in sheet conformation |
liability_score |
float | None
|
liability score (lower is better) |
liability_num_violations |
int | None
|
number of liability violations |
liability_high_severity_violations |
int | None
|
number of high-severity liability violations |
min_interaction_pae |
float | None
|
minimum predicted aligned error at the interface |
delta_sasa_refolded |
float | None
|
change in solvent-accessible surface area upon binding (A^2) |
plip_hbonds_refolded |
int | None
|
number of hydrogen bonds at the interface |
plip_saltbridge_refolded |
int | None
|
number of salt bridges at the interface |
num_tokens |
int | None
|
number of tokens in the design |
design_hydrophobicity |
float | None
|
hydrophobicity of the designed binder |
num_filters_passed |
int | None
|
number of quality filters passed |
ProteinBinder
dataclass
ProteinBinder(bound_structure_uuid: str | None = None, sequence: str | None = None, scores: BinderScores | None = None)
Generated protein binder design.
Attributes:
| Name | Type | Description |
|---|---|---|
bound_structure_uuid |
str | None
|
UUID of the bound structure (binder + target complex) |
sequence |
str | None
|
amino acid sequence of the designed binder |
scores |
BinderScores | None
|
detailed scores for the binder design |
ProteinBinderDesignResult
dataclass
ProteinBinderDesignResult(workflow_data: dict[str, Any], workflow_type: str, workflow_uuid: str, complete: bool = True)
Bases: WorkflowResult
Result from a protein-binder-design workflow.
submit_protein_binder_design_workflow
submit_protein_binder_design_workflow(binder_design_input: dict[str, Any], protocol: BinderProtocol | str = BinderProtocol.PROTEIN_ANYTHING, num_designs: int = 10, budget: int = 2, name: str = 'Protein Binder Design Workflow', folder_uuid: str | None = None, folder: Folder | None = None, max_credits: int | None = None, webhook_url: str | None = None, is_draft: bool = False) -> Workflow[ProteinBinderDesignResult]
Submits a protein-binder-design workflow to the API.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
binder_design_input
|
dict[str, Any]
|
input specification for the binder design (BoltzGenInput format) |
required |
protocol
|
BinderProtocol | str
|
design protocol to use. Options: - PROTEIN_ANYTHING: Design a protein binder - PEPTIDE_ANYTHING: Design a peptide binder - PROTEIN_SMALL_MOLECULE: Design a protein that binds a small molecule - NANOBODY_ANYTHING: Design a nanobody binder |
PROTEIN_ANYTHING
|
num_designs
|
int
|
number of designs to generate |
10
|
budget
|
int
|
number of designs to return in the final diversity-optimized set |
2
|
name
|
str
|
name of the workflow |
'Protein Binder Design Workflow'
|
folder_uuid
|
str | None
|
UUID of the folder to place the workflow in |
None
|
folder
|
Folder | None
|
destination folder |
None
|
max_credits
|
int | None
|
maximum credits for the workflow |
None
|
webhook_url
|
str | None
|
URL that Rowan will POST to when the workflow completes |
None
|
is_draft
|
bool
|
save as a draft without starting execution |
False
|
Returns:
| Type | Description |
|---|---|
Workflow[ProteinBinderDesignResult]
|
submitted workflow |
Raises:
| Type | Description |
|---|---|
ValueError
|
protocol is not a valid BinderProtocol, or if no protein_entities sequence contains a designable region |
HTTPStatusError
|
request to the API fails |