Documentation | NovoMCP

Documentation

Everything you need to connect Claude to molecular intelligence.

Contents

Quick Start

NovoMCP is a remote MCP server with OAuth support that works on all Claude platforms: web, desktop, mobile, and API.

All Platforms (OAuth) — Easiest

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

NovoMCP uses OAuth 2.0 for authentication. No config files or headers needed—just add the URL and authenticate in your browser.

Claude Desktop (Config File Alternative)

If you prefer manual configuration:

{ "mcpServers": { "novomcp": { "url": "https://ai.novomcp.com", "headers": { "X-API-Key": "nmcp_your-api-key" } } } }

Config file locations:

  • macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
  • Windows: %APPDATA%\Claude\claude_desktop_config.json

Restart Claude Desktop after saving.

Platform support: Claude.ai web (Pro/Max/Team/Enterprise), Claude Desktop (all plans), Claude Mobile iOS/Android (Pro/Max/Team/Enterprise), Claude API.

Authentication

NovoMCP supports two authentication methods:

OAuth 2.0 (Recommended)

When you add NovoMCP as a custom connector, Claude automatically uses OAuth. You'll be redirected to a login page where you enter your API key. This is the simplest setup—no headers or config files needed.

API Key Header (Direct Access)

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

Getting a Key

Request access via email. Keys are provisioned within 24 hours. Each key includes:

  • Organization ID and name
  • Access tier (Free, Pro, Team, or Enterprise)
  • Daily query limit based on tier

Key Format

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

Rate limits: Requests are rate-limited per organization. Free tier: 100/day. Pro: 1,000/day. Team: 10,000/day. Enterprise: unlimited.

Tool Reference

NovoMCP exposes 21 tools, 5 resources, and 4 prompts via the Model Context Protocol. Claude can invoke these directly.

Free Tier (4 tools)

get_molecule_profile 2 credits
Retrieve comprehensive molecular profile including properties, ADMET predictions, and regulatory compliance status.
Parameters: identifier (SMILES, CID, or name)
get_molecule_info 1 credit
Basic molecular properties via RDKit: molecular weight, LogP, TPSA, hydrogen bond donors/acceptors, rotatable bonds.
Parameters: smiles
get_platform_info 0 credits
Platform information: subscription tiers, database statistics, ADMET capabilities, compliance lists, usage summary.
Parameters: info_type (all, tiers, database, admet, compliance, usage)
get_job_status 0 credits
Check status of async jobs (structure prediction, molecular dynamics). Always free.
Parameters: job_id

Pro Tier (+9 tools)

search_similar 5 credits
Find structurally similar molecules using Tanimoto similarity. Returns top matches with similarity scores.
Parameters: smiles, threshold (0.0-1.0), limit
filter_molecules 5 credits
Filter database by property ranges. Supports molecular weight, LogP, QED, TPSA. Exclude controlled substances.
Parameters: filters (object), limit
batch_profile 10 credits
Profile multiple molecules in a single request. Up to 100 compounds per call.
Parameters: identifiers (array)
calculate_properties 10 credits
On-demand RDKit property calculation: MW, exact mass, LogP, LogD, TPSA, SA Score, Lipinski/Veber violations, QED.
Parameters: smiles
search_literature 5 credits
Semantic search across 14,000+ curated drug discovery papers. Returns titles, authors, DOIs, relevance scores.
Parameters: query, top_k
search_patents 5 credits
Search 2,400+ USPTO pharmaceutical patents. Returns patent numbers, applicants, abstracts, relevance scores.
Parameters: query, top_k
search_biorxiv 3 credits
Search bioRxiv/medRxiv preprint servers for latest research. 250k+ preprints with full metadata.
Parameters: query (e.g., "BRAF inhibitors"), server (biorxiv/medrxiv), top_k, days_back
search_chembl 5 credits
Search ChEMBL database for compounds, targets, and bioactivity. 2.4M compounds with SMILES and activity data.
Parameters: query (e.g., "Osimertinib"), search_type (compound/target/activity), top_k
search_clinical_trials 3 credits
Search ClinicalTrials.gov for clinical studies. 500k+ trials with status, phase, and enrollment.
Parameters: query (e.g., "obesity treatment"), status, phase, top_k

Pro Tip: Use search_literature, search_patents, search_biorxiv, and search_clinical_trials together to build a comprehensive landscape analysis for a specific target or compound.

Team Tier (+5 tools)

optimize_molecule 25 credits
Generate optimized molecular variants using NVIDIA MolMIM. Target specific properties. All outputs screened for compliance.
Parameters: smiles, target_qed, target_logp, num_variants
predict_structure 100 credits
Predict 3D protein structure from amino acid sequence via OpenFold3. Async—returns job ID.
Parameters: sequence, name
get_structure_result 0 credits
Retrieve completed structure predictions. Check status and download PDB files with confidence scores.
Parameters: job_id
predict_admet 20 credits
40+ ML-based ADMET predictions: cardiotoxicity (1d/5d/10d/30d), CYP450 inhibition, nuclear receptors, hepatotoxicity, Ames.
Parameters: smiles
get_3d_properties 15 credits
32+ 3D molecular properties from conformer generation: geometry (radius of gyration), energy, electrostatics (dipole), surface/volume.
Parameters: smiles, include_coordinates

Enterprise Tier (+2 tools)

check_compliance 3 credits
Full FAVES regulatory assessment with context-aware evaluation for intended use case.
Parameters: smiles, context
screen_library 50 credits
Screen compound libraries up to 1000 molecules with optional full FAVES assessment and filtering.
Parameters: identifiers (array), filters, full_faves

Resources

NovoMCP exposes 5 resources that provide static and dynamic data. Access via GET /mcp/resources.

compliance_schedules
DEA Schedule I-V substances, CWC chemical weapons lists, FDA banned substances, EPA PBT chemicals, and EU REACH restricted compounds.
admet_properties
List of 40+ ADMET property predictions available: absorption, distribution, metabolism, excretion, and toxicity endpoints.
tier_features
Features available at each subscription tier (Free, Pro, Team, Enterprise) with daily limits and tool access details.
database_stats
Current database statistics: 122M indexed molecules, 14,398 curated papers, 2,416 USPTO patents. Updated periodically.
changelog
Recent changes to NovoMCP tools, features, and API. Check this if tools seem missing—you may need to reconnect your MCP connection to refresh the tool list.

Prompts

NovoMCP provides 4 pre-defined prompts for common workflows. Access via GET /mcp/prompts.

quick_check
Quickly check if a molecule is a controlled substance or has safety flags. Returns compliance status and any alerts.
Arguments: smiles (required)
full_analysis
Comprehensive molecular analysis including properties, ADMET predictions, compliance status, and drug-likeness scores.
Arguments: smiles (required)
find_alternatives
Find structurally similar molecules that pass compliance checks. Useful when a lead compound is flagged.
Arguments: smiles (required), min_similarity (optional, default 0.7)
literature_review
Search drug discovery papers and patents for a topic or target. Returns relevant literature with citations.
Arguments: query (required), max_results (optional, default 10)

Examples

Ask Claude naturally. NovoMCP tools are invoked automatically.

Basic Profiling

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

Claude invokes get_molecule_profile with identifier "ibuprofen" and receives:

Response
{ "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 Example Prompts

Try these with Claude:

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

→ Invokes optimize_molecule with QED and LogP targets

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

→ Invokes get_molecule_profile to check DEA, FDA, structural alerts

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

→ Invokes search_literature and search_clinical_trials

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

→ Invokes search_similar with exclude_flagged=true

Pro Tip — Landscape Analysis: Combine search_literature, search_patents, search_biorxiv, and search_clinical_trials to build a comprehensive research landscape for any target or therapeutic area. Just ask Claude: "Give me a complete landscape analysis of KRAS inhibitors."

Novel molecules: If a compound isn't in our database, NovoMCP computes properties on-the-fly using RDKit and runs FAVES screening. Response times may be slightly longer (~500ms vs ~50ms).