Collaborative Drug Discovery Deep Learning Bioisosteres API
Deep learning bioisostere suggestions
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OpenAPI Specification
openapi: 3.2.0
info:
contact:
url: https://support.collaborativedrug.com/hc/en-us/requests/new
description: 'Collaborative Drug Discovery provides an API (Application Programming
Interface) that can be used for secure programmatic access to your vault
data.'
license:
name: Proprietary
url: https://support.collaborativedrug.com/hc/en-us/requests/new
title: CDD Deep Learning Bioisosteres API
version: 1.0.0
servers:
- url: https://app.collaborativedrug.com/api/v1
security:
- ApiKeyAuth: []
tags:
- description: Deep learning bioisostere suggestions
name: Deep Learning Bioisosteres
paths:
/vaults/{vault_id}/ai/bioisosteres:
post:
summary: Find bioisosteric replacements (hierarchical)
tags:
- Deep Learning Bioisosteres
operationId: ai_bioisosteres
description: Submit a chemical structure and receive bioisosteric replacement suggestions grouped by fragment. Requires the vault to have Deep Learning enabled.
security: []
parameters:
- name: vault_id
in: path
required: true
description: ID of the current vault.
schema:
type: integer
- name: X-CDD-Token
in: header
required: true
description: API key token for authentication.
schema:
type: string
responses:
'200':
description: Success — returns bioisosteric suggestions grouped by fragment.
content:
application/json:
schema:
type: object
required:
- status
- result
properties:
status:
type: string
example: OK
mocked_service:
type: boolean
description: true only on the dev mock, not the real service
result:
type: object
required:
- query
- suggestions
properties:
query:
type: string
example: Clc1ccc(COC(Cn2ccnc2)c2ccc(Cl)cc2Cl)c(Cl)c1
suggestions:
type: array
items:
type: object
required:
- fragment
- size
- atom_indices
- bioisosteres
properties:
fragment:
type: string
example: '[16*]c1ccc(Cl)cc1Cl'
size:
type: integer
example: 8
atom_indices:
type: array
items:
type: integer
example:
- 0
- 1
bioisosteres:
type: array
items:
type: object
required:
- fragment
- structure
- synthetic_feasibility
- tanimoto
- atom_indices
properties:
fragment:
type: string
example: '[16*]c1ccc(F)cc1Cl'
inchikey:
type: string
example: QCNPSEBNVBYHLY-UHFFFAOYSA-N
structure:
type: string
example: c1ccncc1
tanimoto:
type: number
format: float
example: 0.875
atom_indices:
type: array
items:
type: integer
example:
- 0
- 1
synthetic_feasibility:
type: object
required:
- synthetic_feasibility_score
- profile_overlap
- bits_missing
- fraction_missing
properties:
synthetic_feasibility_score:
type: number
format: float
example: 0.9
profile_overlap:
type: number
format: float
example: 0.8
bits_missing:
type: number
format: float
example: 0.1
fraction_missing:
type: number
format: float
example: 0.2
alerts:
type: array
items:
type: object
required:
- filter_set
- description
properties:
filter_set:
type: string
example: Brenk
description:
type: string
example: aniline
identifiers:
type: array
items:
type: object
required:
- name
- collection
properties:
name:
type: string
example: SCHEMBL11832241
collection:
type: string
example: SureChEMBL
patent:
type: object
required:
- count
- first_patent
- first_date
properties:
count:
type: integer
example: 1
first_date:
type: string
format: date
example: '1976-01-20'
first_patent:
type: string
example: US-3933824-A
cdd_public:
type: object
required:
- molecule_id
properties:
molecule_id:
type: integer
example: 123456
cdd_private:
type: object
required:
- id
- standard_inchi_key
- exact
properties:
id:
type: integer
example: 123456
standard_inchi_key:
type: string
example: QCNPSEBNVBYHLY-UHFFFAOYSA-N
exact:
type: boolean
example: true
'400':
description: Bad request — missing or invalid parameters.
content:
application/json:
schema:
type: object
required:
- error
- code
properties:
error:
type: string
example: structure parameter is required
code:
type: integer
example: 400
'401':
description: Unauthorized — Deep Learning not enabled for this vault or user lacks access.
content:
application/json:
schema:
type: object
required:
- error
- code
properties:
error:
type: string
example: Dl bioisosteres endpoint only accessible in vaults with Deep Learning enabled
code:
type: integer
example: 401
requestBody:
content:
application/json:
schema:
type: object
required:
- structure
properties:
structure:
type: string
description: SMILES or MOL representation of structure to find bioisosteric replacements for.
example: Clc1ccc(COC(Cn2ccnc2)c2ccc(Cl)cc2Cl)c(Cl)c1
number_suggestions:
type: integer
description: Number of bioisosteric suggestions per fragment. Defaults to 5, max 200.
example: 5
return_known_identifiers:
type: boolean
description: Include known identifiers (InChIKey, etc.) in response. Defaults to false.
example: false
lookup_internal_identifiers:
type: boolean
description: Opt in to server-side enrichment with internal vault identifiers. When true, each bioisostere's InChIKey is used to find molecules in the Vault. The 14-character prefix of the InChIKey is used to catch stereochemical variants. The internal identifiers are appended to the identifiers array as an `Internal` collection. Defaults to false.
example: false
filter_structure_alerts:
type: boolean
description: Filter out suggestions with additional structural alerts. Defaults to true.
example: true
filter_by_atom_indices:
type: array
items:
type: integer
description: List of atom indices identifying which fragments to include in fragmentation. Each suggestion fragment whose `atom_indices` overlaps this list is kept. If omitted, all fragments are used.
example:
- 0
- 1
required: true
/vaults/{vault_id}/ai/bioisosteres/flat:
post:
summary: Find bioisosteric replacements (flat list)
tags:
- Deep Learning Bioisosteres
operationId: ai_bioisosteres_flat
description: Submit a chemical structure and receive bioisosteric replacement suggestions as a flat list. Requires the vault to have Deep Learning enabled.
security: []
parameters:
- name: vault_id
in: path
required: true
description: ID of the current vault.
schema:
type: integer
- name: X-CDD-Token
in: header
required: true
description: API key token for authentication.
schema:
type: string
responses:
'200':
description: Success — returns bioisosteric suggestions as a flat list.
content:
application/json:
schema:
type: object
required:
- query
- suggestions
properties:
query:
type: string
example: Clc1ccc(COC(Cn2ccnc2)c2ccc(Cl)cc2Cl)c(Cl)c1
suggestions:
type: array
items:
type: object
required:
- structure
- fragment
- replacement_fragment
- tanimoto
- alerts
properties:
structure:
type: string
example: Fc1ccc(-c2n[nH]c3c2CCNCC3)cc1F
fragment:
type: string
example: '[16*]c1ccc(Cl)cc1Cl'
replacement_fragment:
type: string
example: '[16*]c1ccc(F)cc1F'
tanimoto:
type: number
format: float
example: 0.875
synthetic_feasibility_score:
type: number
format: float
example: 0.9
identifiers:
type: string
example: SCHEMBL11832241, CHEMBL12345678
alerts:
type: string
example: acid_halide,carbonyl_halide
'400':
description: Bad request — missing or invalid parameters.
content:
application/json:
schema:
type: object
required:
- error
- code
properties:
error:
type: string
example: structure parameter is required
code:
type: integer
example: 400
'401':
description: Unauthorized — Deep Learning not enabled for this vault or user lacks access.
content:
application/json:
schema:
type: object
required:
- error
- code
properties:
error:
type: string
example: Dl bioisosteres endpoint only accessible in vaults with Deep Learning enabled
code:
type: integer
example: 401
requestBody:
content:
application/json:
schema:
type: object
required:
- structure
properties:
structure:
type: string
description: SMILES or MOL representation of structure to find bioisosteric replacements for.
example: Clc1ccc(COC(Cn2ccnc2)c2ccc(Cl)cc2Cl)c(Cl)c1
number_suggestions:
type: integer
description: Number of bioisosteric suggestions per fragment. Defaults to 5, max 200.
example: 5
return_known_identifiers:
type: boolean
description: Include known identifiers (InChIKey, etc.) in response. Defaults to false.
example: false
lookup_internal_identifiers:
type: boolean
description: Opt in to server-side enrichment with internal vault identifiers. When true, each bioisostere's InChIKey is used to find molecules in the Vault. The 14-character prefix of the InChIKey is used to catch stereochemical variants. The internal identifiers are appended to the identifiers array as an `Internal` collection. Defaults to false.
example: false
filter_structure_alerts:
type: boolean
description: Filter out suggestions with additional structural alerts. Defaults to true.
example: true
filter_by_atom_indices:
type: array
items:
type: integer
description: List of atom indices identifying which fragments to include in fragmentation. Each suggestion fragment whose `atom_indices` overlaps this list is kept. If omitted, all fragments are used.
example:
- 0
- 1
required: true
/vaults/{vault_id}/ai/bioisosteres/get_fragmentation:
post:
summary: Fragment a chemical structure
tags:
- Deep Learning Bioisosteres
operationId: ai_bioisosteres_get_fragmentation
description: Submit a chemical structure and receive its fragmentation without bioisosteric suggestions. Requires the vault to have Deep Learning enabled.
security: []
parameters:
- name: vault_id
in: path
required: true
description: ID of the current vault.
schema:
type: integer
- name: X-CDD-Token
in: header
required: true
description: API key token for authentication.
schema:
type: string
responses:
'200':
description: Success — returns the fragmentation of the structure.
content:
application/json:
schema:
type: object
required:
- status
- result
properties:
status:
type: string
example: OK
mocked_service:
type: boolean
description: true only on the dev mock, not the real service
result:
type: object
required:
- query
- suggestions
properties:
query:
type: string
example: Clc1ccc(COC(Cn2ccnc2)c2ccc(Cl)cc2Cl)c(Cl)c1
suggestions:
type: array
items:
type: object
required:
- fragment
- size
- atom_indices
properties:
fragment:
type: string
example: '[16*]c1ccc(Cl)cc1Cl'
size:
type: integer
example: 8
atom_indices:
type: array
items:
type: integer
example:
- 0
- 1
'400':
description: Bad request — missing or invalid parameters.
content:
application/json:
schema:
type: object
required:
- error
- code
properties:
error:
type: string
example: structure parameter is required
code:
type: integer
example: 400
'401':
description: Unauthorized — Deep Learning not enabled for this vault or user lacks access.
content:
application/json:
schema:
type: object
required:
- error
- code
properties:
error:
type: string
example: Dl bioisosteres endpoint only accessible in vaults with Deep Learning enabled
code:
type: integer
example: 401
requestBody:
content:
application/json:
schema:
type: object
required:
- structure
properties:
structure:
type: string
description: SMILES or MOL representation of structure to fragment.
example: Clc1ccc(COC(Cn2ccnc2)c2ccc(Cl)cc2Cl)c(Cl)c1
required: true
components:
securitySchemes:
ApiKeyAuth:
in: header
name: X-CDD-Token
type: apiKey