NVIDIA NIM

NVIDIA NIM Biology (BioNeMo) API

BioNeMo NIMs for protein structure prediction (AlphaFold2, ESMFold, OpenFold), protein generation (ProtGPT2, RFDiffusion), molecular property prediction (MolMIM), small molecule generation, and molecular docking (DiffDock). Each model is a containerized microservice with the same OpenAPI surface.

Documentation GitHub OpenAPI

Operations 3

POST /v1/biology/nvidia/alphafold2/predict-structure-from-sequence Predict Protein Structure #

POST /v1/biology/mit/diffdock Dock Ligand To Protein #

POST /v1/biology/nvidia/molmim/generate Generate Small Molecules #

Documentation

📖

Documentation

https://docs.nvidia.com/nim/bionemo/latest/index.html

Specifications

⚙

OpenAPI

https://raw.githubusercontent.com/api-evangelist/nvidia-nim/refs/heads/main/openapi/nvidia-nim-biology-api-openapi.yml

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OpenAPI Specification

openapi: 3.2.0
info:
  title: NVIDIA NIM (BioNeMo) ASR Biology API
  description: 'NVIDIA BioNeMo NIMs for drug discovery and structural biology. Each model is a containerized microservice with its own task-specific payload but a consistent JSON contract. Includes protein structure prediction (AlphaFold2, ESMFold, OpenFold), protein generation (ProtGPT2, RFDiffusion), molecular property prediction (MolMIM), small molecule generation, and molecular docking (DiffDock).

    '
  version: '2026-05-25'
  contact:
    name: NVIDIA Developer Support
    url: https://forums.developer.nvidia.com/c/ai-data-science/nemo-llm-service/
  license:
    name: NVIDIA AI Enterprise License
    url: https://www.nvidia.com/en-us/data-center/products/ai-enterprise/
servers:
- url: https://integrate.api.nvidia.com
  description: NVIDIA-hosted NIM endpoint
- url: http://localhost:8000
  description: Self-hosted NIM container default
security:
- BearerAuth: []
tags:
- name: Biology
  description: Protein, molecule, and structural-biology operations
paths:
  /v1/biology/nvidia/alphafold2/predict-structure-from-sequence:
    post:
      summary: Predict Protein Structure
      description: Predict the 3D structure of a protein from its amino acid sequence using AlphaFold2 NIM.
      operationId: predictProteinStructure
      tags:
      - Biology
      requestBody:
        required: true
        content:
          application/json:
            schema:
              type: object
              required:
              - sequence
              properties:
                sequence:
                  type: string
                  description: Single-letter amino acid sequence.
                databases:
                  type: array
                  items:
                    type: string
                  description: MSA databases to use (e.g. `uniref90`, `mgnify`, `small_bfd`).
                relax_prediction:
                  type: boolean
                  default: true
      responses:
        '200':
          description: Predicted structure.
          content:
            application/json:
              schema:
                type: object
                properties:
                  pdbs:
                    type: array
                    items:
                      type: string
                      description: PDB-format structure.
        '400':
          description: Invalid sequence.
        '401':
          description: Missing or invalid API key.
  /v1/biology/mit/diffdock:
    post:
      summary: Dock Ligand To Protein
      description: Predict the binding pose of a small molecule ligand against a protein using DiffDock NIM.
      operationId: dockLigand
      tags:
      - Biology
      requestBody:
        required: true
        content:
          application/json:
            schema:
              type: object
              required:
              - protein
              - ligand
              properties:
                protein:
                  type: string
                  description: PDB-format protein structure.
                ligand:
                  type: string
                  description: SDF or SMILES ligand representation.
                num_poses:
                  type: integer
                  default: 10
                time_divisions:
                  type: integer
                  default: 20
                steps:
                  type: integer
                  default: 18
      responses:
        '200':
          description: Predicted binding poses.
          content:
            application/json:
              schema:
                type: object
                properties:
                  ligand_positions:
                    type: array
                    items:
                      type: string
                  position_confidence:
                    type: array
                    items:
                      type: number
        '400':
          description: Invalid input.
  /v1/biology/nvidia/molmim/generate:
    post:
      summary: Generate Small Molecules
      description: Generate small molecule SMILES around a seed molecule using NVIDIA MolMIM NIM.
      operationId: generateMolecules
      tags:
      - Biology
      requestBody:
        required: true
        content:
          application/json:
            schema:
              type: object
              required:
              - smi
              properties:
                smi:
                  type: string
                  description: Seed SMILES string.
                algorithm:
                  type: string
                  enum:
                  - CMA-ES
                num_molecules:
                  type: integer
                  default: 10
                property_name:
                  type: string
                  enum:
                  - QED
                  - plogP
                minimize:
                  type: boolean
                min_similarity:
                  type: number
                  default: 0.3
                particles:
                  type: integer
                  default: 30
                iterations:
                  type: integer
                  default: 10
      responses:
        '200':
          description: Generated molecules.
          content:
            application/json:
              schema:
                type: object
                properties:
                  generated:
                    type: array
                    items:
                      type: object
                      properties:
                        sample:
                          type: string
                        score:
                          type: number
components:
  securitySchemes:
    BearerAuth:
      type: http
      scheme: bearer
      bearerFormat: nvapi-...