Quick Start

NovoMCP is a remote MCP server with OAuth support that works with any MCP-compatible AI client: Claude, ChatGPT, Cursor, Windsurf, GitHub Copilot, and more.

Prerequisites: A NovoMCP API key (get started free at app.novomcp.com) and an MCP-compatible AI client.

Claude Desktop / Web / Mobile

1. Go to Settings > Connectors
2. Click "Add custom connector"
3. Enter URL: https://www.novoquantnexus.com/novomcp/mcp
4. Click Connect — a login page opens in your browser
5. Enter your NovoMCP API key (nmcp_...)
6. Click Authorize Access — done!

Claude Code (Terminal)

1. claude mcp add --transport http novomcp https://www.novoquantnexus.com/novomcp/mcp
2. claude
3. /mcp  → authenticate in browser
4. Done! 27 tools now available

Auth tokens are stored in your system keychain and refresh automatically on future sessions.

Team Setup (.mcp.json)

For teams, add NovoMCP to your repo's .mcp.json so every team member gets it automatically:

{
  "mcpServers": {
    "novomcp": {
      "type": "http",
      "url": "https://www.novoquantnexus.com/novomcp/mcp"
    }
  }
}

Each team member still authenticates individually via /mcp on first use.

Cursor / Windsurf

1. Open Settings → MCP (or equivalent)
2. Add server URL: https://www.novoquantnexus.com/novomcp/mcp
3. Authenticate with your API key
4. Done — all 27 tools available in chat

Other MCP Clients

Server URL: https://www.novoquantnexus.com/novomcp/mcp
Transport:  Streamable HTTP
Auth:       OAuth 2.0 (automatic) or API key header

Try it

Once connected, ask your AI:

"What's the ADMET profile of aspirin? Is it hepatotoxic?"

Authentication

NovoMCP supports two authentication methods:

OAuth 2.0 (Recommended)

When you add NovoMCP as a connector, your client automatically uses OAuth. You'll be redirected to a login page where you enter your API key. No headers or config files needed.

API Key Header

For programmatic access, pass your API key in the X-API-Key header or Authorization: Bearer header.

Key Format: Keys follow the format nmcp_[random]. Store securely — keys cannot be retrieved after creation.

Tool Reference

NovoMCP exposes 27 tools, 5 resources, and 4 prompts via the Model Context Protocol. Your AI client invokes these automatically.

Molecular Intelligence

get_molecule_profileRetrieve comprehensive molecular profile including properties, ADMET predictions, and regulatory compliance status.

get_molecule_infoBasic molecular properties via RDKit: molecular weight, LogP, TPSA, hydrogen bond donors/acceptors, rotatable bonds.

calculate_propertiesOn-demand RDKit property calculation: MW, exact mass, LogP, LogD, TPSA, SA Score, Lipinski/Veber violations, QED.

get_3d_properties32+ 3D molecular properties from conformer generation: geometry, energy, electrostatics, surface/volume.

search_similarFind structurally similar molecules using Tanimoto similarity. Returns top matches with similarity scores.

filter_moleculesFilter database by property ranges. Supports molecular weight, LogP, QED, TPSA. Exclude controlled substances.

batch_profileProfile multiple molecules in a single request. Up to 100 compounds per call.

optimize_moleculeGenerate optimized molecular variants using NVIDIA MolMIM. Target specific properties. All outputs screened for compliance.

ADMET & FAVES Compliance

FAVES screens every molecule against eight regulatory jurisdictions — DEA, FDA, EPA, CWC, EU REACH — as part of the prediction, not as a separate step.

predict_admet40+ ML-based ADMET predictions: cardiotoxicity, CYP450 inhibition, nuclear receptors, hepatotoxicity, Ames.

check_complianceFull FAVES regulatory assessment with context-aware evaluation for intended use case.

screen_libraryScreen compound libraries up to 1000 molecules with optional full FAVES assessment and filtering.

Structure Prediction

get_protein_structureSmart protein structure resolver. Accepts names (EGFR, CDK2), PDB IDs (1M17), or sequences. Returns experimental structures or OpenFold3 predictions.

predict_structurePredict 3D protein structure from amino acid sequence via OpenFold3. Async — returns job ID.

get_structure_resultRetrieve completed structure predictions. Check status and download PDB files with confidence scores.

Literature & Data Search

search_literatureSemantic search across 14,000+ curated drug discovery papers. Returns titles, authors, DOIs, relevance scores.

search_patentsSearch 2,400+ USPTO pharmaceutical patents. Returns patent numbers, applicants, abstracts.

search_biorxivSearch bioRxiv/medRxiv preprint servers for latest research. 250k+ preprints with full metadata.

search_chemblSearch ChEMBL database for compounds, targets, and bioactivity. 2.4M compounds with SMILES and activity data.

search_clinical_trialsSearch ClinicalTrials.gov for clinical studies. 500k+ trials with status, phase, and enrollment.

Data Connectors & Platform

pull_from_sourceBidirectional data pipeline: pull compounds from Databricks/Snowflake, run ADMET + FAVES processing, push enriched results back.

push_to_destinationList connections, discover schemas, preview mappings, export results to Snowflake, BigQuery, Databricks, Supabase.

get_platform_infoPlatform information: database statistics, ADMET capabilities, compliance lists.

get_job_statusCheck status of async jobs (structure prediction, molecular dynamics).

get_credit_usageCheck your credit balance, usage statistics, and research value realized.

Resources

5 resources that provide static and dynamic data.

compliance_schedulesDEA Schedule I-V, CWC chemical weapons lists, FDA banned substances, EPA PBT chemicals, EU REACH restricted compounds.

admet_propertiesList of 40+ ADMET property predictions available: absorption, distribution, metabolism, excretion, toxicity endpoints.

tier_featuresFeatures available at each subscription tier with tool access details.

database_statsCurrent database statistics: 122M indexed molecules, 14,398 curated papers, 2,416 USPTO patents.

changelogRecent changes to NovoMCP tools, features, and API.

Prompts

4 pre-defined prompts for common workflows.

quick_checkQuickly check if a molecule is a controlled substance or has safety flags.

full_analysisComprehensive molecular analysis including properties, ADMET predictions, compliance, and drug-likeness.

find_alternativesFind structurally similar molecules that pass compliance checks.

literature_reviewSearch drug discovery papers and patents for a topic or target.

Enterprise Connectors

Export molecular intelligence data directly to your data warehouse. 4 connector adapters with OAuth sign-in, dynamic schema discovery, AI-assisted field mapping, and full governance.

Snowflake

Databricks

BigQuery (OAuth)

Supabase

How It Works

1. Discover

discover_schema introspects the target system — tables, columns, types — and normalizes to 5 standard types.

2. Map

preview_mapping aligns NovoMCP tool output to target columns. Template, auto-matching, or AI-assisted mapping.

3. Export

export_results writes data through the appropriate connector adapter.

Governance: All connector credentials are stored in Azure Key Vault — never in the database. All export operations are audit-logged with full traceability.

Connector Setup

BigQuery (OAuth)

Click “Connect with Google” in the connections dashboard. You'll be redirected to Google's consent screen. No API keys or service accounts needed. Tokens refresh automatically.

Snowflake

Provide your account identifier (e.g. xy12345.us-east-1), username, and password. Specify a warehouse, database, and schema.

Databricks

Generate a personal access token in Databricks: User Settings > Developer > Access Tokens. Provide the token with your workspace URL and target catalog/schema.

Supabase

Find connection details in your Supabase project dashboard under Settings > Database > Connection String. Use the service_role key for full access.

Examples

Ask in natural language. NovoMCP tools are selected and invoked automatically.

Basic Profiling

"What's the ADMET profile of ibuprofen? Is it hepatotoxic?"

Response includes properties, ADMET predictions, and compliance status:

{
  "properties": {
    "cid": 3672,
    "smiles": "CC(C)CC1=CC=C(C=C1)C(C)C(=O)O",
    "molecular_weight": 206.28,
    "logp": 3.97,
    "tpsa": 37.3,
    "qed": 0.72
  },
  "admet": {
    "hepatotoxicity_probability": 0.12,
    "cardiotoxicity_probability": 0.08,
    "bbb_permeant": true,
    "cyp2d6_inhibitor": false,
    "human_intestinal_absorption": 0.98
  },
  "compliance": {
    "status": "clear",
    "is_dea_controlled": false,
    "is_fda_banned": false,
    "structural_alerts": []
  }
}

More Examples

"Optimize this lead compound for better oral bioavailability while maintaining selectivity: CC1=CC=C(C=C1)C(=O)NC2=CC=CC=C2"

→ optimize_molecule — generates variants targeting QED and LogP

"Is this molecule safe to develop? Check for any regulatory concerns: CN1C=NC2=C1C(=O)N(C(=O)N2C)C"

→ get_molecule_profile — returns DEA, FDA, structural alert status

"What's known about CDK4/6 inhibitors in breast cancer? Show me literature and clinical trials."

→ search_literature + search_clinical_trials — parallel search

"Find molecules similar to palbociclib with QED > 0.6 and no PAINS alerts"

→ search_similar — similarity search with property and compliance filters

Novel molecules: Compounds not in the pre-computed database are processed on-the-fly via RDKit with FAVES screening. Response times: ~500ms vs ~50ms for indexed compounds.