medchem

Filter and prioritize compound libraries using Python medicinal chemistry rules.

Updated May 17, 2026
One-click install
npx skills add https://github.com/galeep/plugin-place --skill medchem-galeep
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: medchem
Source: https://github.com/galeep/plugin-place/tree/main/plugins/sci-cheminformatics-drug-discovery/skills/medchem
Command: npx skills add https://github.com/galeep/plugin-place --skill medchem-galeep

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires medchem, datamol, and includes scripts (resource) and references (resource) components.

What problem does it solve?

Medchem addresses the challenge of efficiently filtering and prioritizing compound libraries in drug discovery by applying a suite of medicinal chemistry rules, structural alerts, complexity metrics, and a custom query language.

Core Features & Use Cases

  • Medicinal Chemistry Rules: Apply Lipinski, Veber, CNS, and other drug-likeness rules.
  • Structural Alert Filters: Identify problematic patterns using PAINS, NIBR, and ChEMBL rules.
  • Complexity Metrics: Calculate and filter compounds based on molecular complexity.
  • Functional API: Provides one-call wrappers for common operations, simplifying filtering workflows.
  • Use Case: Imagine you have a large compound library and want to prioritize it based on drug-likeness and structural alert rules to quickly identify potential drug candidates.

Quick Start

Use the medchem skill to apply the rule of five and PAINS filters to the compound library 'library.sdf'.

Frequently Asked Questions about medchem

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

FAQPage Schema
How do I filter a compound library for drug discovery?

Filter a compound library by applying medicinal chemistry rules, structural alerts, and complexity metrics to prioritize drug candidates. This process uses drug-likeness filters like Lipinski and Veber for compound triage.

What is compound triage and library prioritization in medicinal chemistry?

Compound triage and library prioritization in medicinal chemistry involves filtering large sets of molecules using drug-likeness rules, structural alert detection, and complexity metrics to identify the most promising drug discovery candidates.

How do I apply PAINS and Lipinski filters to an SDF file?

Apply PAINS and Lipinski filters to an SDF file using functional API one-call wrappers. This automates the structural alert detection and drug-likeness filtering workflow for compound triage and library prioritization.

Does compound triage require Python libraries like datamol and medchem?

Compound triage requires Python libraries like datamol and medchem to automate medicinal chemistry filtering workflows. These dependencies provide the functional API and molecular complexity calculations needed for library prioritization.

Can I detect structural alerts like PAINS and NIBR in a compound library?

Detect structural alerts like PAINS and NIBR in a compound library by applying specialized medicinal chemistry filters. This identifies problematic molecular patterns to streamline compound triage and drug discovery workflows.

What's the best way to calculate molecular complexity for compound prioritization?

Calculate molecular complexity for compound prioritization by applying complexity metrics within a Python workflow. This evaluates structural intricacy alongside drug-likeness rules to filter and prioritize large compound libraries efficiently.