drug-discovery

Query ChEMBL, PubChem, OpenFDA, and OpenTargets APIs for compound bioactivity and drug-likeness analysis.

Updated Sep 10, 2026
One-click install
npx skills add https://github.com/loteiron/ZeusAgent --skill drug-discovery-loteiron
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: drug-discovery
Source: https://github.com/loteiron/ZeusAgent/tree/main/optional-skills/research/drug-discovery
Command: npx skills add https://github.com/loteiron/ZeusAgent --skill drug-discovery-loteiron

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve? Pharmaceutical research requires pulling compound, bioactivity, interaction, and safety data from multiple public databases, each with its own API and query syntax. This Skill consolidates those lookups into ready-to-run commands and scripts so researchers can screen molecules and targets without writing API client code. ## Core Features & Use Cases - Bioactive Compound Search: Query ChEMBL by target name or ID and retrieve molecules with pChEMBL activity values, no API key required. - Drug-Likeness Screening: Evaluate compounds against Lipinski's Rule of Five and Veber rules using PubChem property data, including batch screening via the ro5_screen.py script. - Safety & Interaction Lookup: Pull drug interaction text from FDA labels and top reported adverse events from OpenFDA, plus gene-disease associations from OpenTargets. - Use Case: A medicinal chemist evaluating a lead series can batch-screen candidate names for Ro5/Veber compliance, then check the top hit's ChEMBL bioactivity against the intended target and review FDA adverse event reports for related drugs. ## Quick Start Ask the agent to check whether aspirin passes Lipinski's Rule of Five and find active compounds against the EGFR target in ChEMBL.

Frequently Asked Questions about drug-discovery

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I search ChEMBL for compounds active against a target?▼

Query the ChEMBL target search endpoint with a target name like EGFR to get its ChEMBL ID, then request activities filtered by pchembl_value__gte for potency. The included chembl_target.py script automates both steps and lists unique molecules ranked by pChEMBL.

How to check Lipinski Rule of Five for a compound without RDKit?▼

Fetch MolecularWeight, XLogP, HBondDonorCount, and HBondAcceptorCount from the PubChem PUG REST property endpoint, then compare each value against the Ro5 thresholds. The ro5_screen.py script does this in batch for a list of compound names.

Does this require API keys or paid database access?▼

No. ChEMBL, PubChem, OpenFDA, and OpenTargets are all free public APIs requiring no authentication. Only curl and Python's standard library are needed, though ChEMBL batch requests should include a short sleep between calls to respect rate limits.

Can I look up drug interactions and side effects for an approved drug?▼

Yes. The OpenFDA drug label endpoint returns drug_interactions sections from FDA labeling, and the drug event endpoint counts reported adverse reactions by MedDRA term. Note that FDA event data reflects reports, not confirmed causation.

What are the limitations of API-based drug-likeness screening?▼

Property values come from PubChem's computed data, so novel or unnamed structures cannot be screened by name lookup alone. Predictions are rule-based heuristics, and clinical decisions should always be confirmed with a licensed pharmacist or physician.