Collaborative Drug Discovery Deep Learning Similarity API
Deep learning molecular similarity
Work with this as data
Every API here is available over the APIs.io API and to AI agents over MCP.
MCP server
One button, every client — Claude, Cursor, VS Code and the rest.
https://apis.io/mcp
Tools for apis
7 MCP tools reach this
find_apisBrowse and filter every API in the catalog.get_api_artifactsOne API's artifacts, grouped by type.get_openapiThe primary OpenAPI for this API.find_similar_apisAPIs that look like this one.apis_io_searchSTART HERE — APIs, providers and tags for one query, each with its total.resolveTurn a domain, URL or GitHub org into the provider it belongs to.find_cohortsEvery scored population of providers in the catalog.
Call it yourself
curl for this page
This API
curl "https://apis.io/api/v1/apis/collaborative-drug-discovery:collaborative-drug-discovery-deep-learning-similarity-api"
All apis
curl "https://apis.io/api/v1/apis?limit=25"Calls without X-API-Key need no key. Calls with it need a paid plan — get a key.
Get an API key
Free tier, no form to fill in. Signing in shares your email address with us — we store it to create your key and to recognise you if you sign in with another provider. See our Privacy Policy and Terms.
A second provider on the same verified email joins the account you already have.
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 Similarity API
version: 1.0.0
servers:
- url: https://app.collaborativedrug.com/api/v1
security:
- ApiKeyAuth: []
tags:
- description: Deep learning molecular similarity
name: Deep Learning Similarity
paths:
/vaults/{vault_id}/ai/similarity:
post:
summary: Find similar structures using Deep Learning
tags:
- Deep Learning Similarity
operationId: ai_similarity_search
description: Submit a chemical structure and receive a ranked list of similar structures using the Deep Learning similarity model. 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 similar structures ranked by Tanimoto similarity.
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
- query_scaffold
- hits
- metadata
properties:
query:
type: string
example: Nc1ccccc1CCCC
query_scaffold:
type: string
example: c1ccccc1
hits:
type: array
items:
type: object
required:
- structure
- inchikey
- identifiers
- names
- scaffold
- similarity
- tanimoto
- distance
properties:
structure:
type: string
example: Cc1ccncc1
inchikey:
type: string
example: BSYNRYMUTXBXSQ-UHFFFAOYSA-N
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
names:
type: array
items:
type: string
example:
- Compound A
- CDD-123456
scaffold:
type: string
example: c1ccncc1
similarity:
type: number
format: float
example: 0.851
tanimoto:
type: number
format: float
example: 0.123
distance:
type: number
format: float
example: 10.15
metadata:
type: array
items:
type: object
required:
- collection
- search_engine
- metric
- count
- release
properties:
collection:
type: string
example: CDD Public
search_engine:
type: string
example: faiss
metric:
type: string
example: Metric.L2
count:
type: integer
example: 123456
release:
type: string
example: 2024-06
'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 similarity 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 to find similar structures for.
example: c1ccccc1
count:
type: integer
description: Number of similar structures to return. Defaults to 10, max 300.
example: 10
collections:
type: array
items:
type: string
description: List of collection identifiers to filter results by. If omitted, all collections are included.
example:
- SureChEMBL
- ChEMBL
return_patents:
type: boolean
description: Whether to include patent information for compounds in results. Defaults to true.
example: true
lookup_internal_identifiers:
type: boolean
description: Opt in to server-side enrichment with internal vault identifiers. When true, each hit'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
required: true
components:
securitySchemes:
ApiKeyAuth:
in: header
name: X-CDD-Token
type: apiKey