medchem

Filter compound libraries using medicinal chemistry rules and structural alerts.

74|5|Updated Dec 10, 2025
One-click install
npx skills add https://github.com/dralkh/seerai --skill medchem-dralkh
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: medchem
Source: https://github.com/dralkh/seerai/tree/main/skills/medchem
Command: npx skills add https://github.com/dralkh/seerai --skill medchem-dralkh

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Medchem helps researchers rapidly screen compound libraries so they can remove problematic molecules, prioritize promising candidates, and apply consistent medicinal chemistry rules without manual review.

Core Features & Use Cases

  • Drug-likeness filtering: Apply rules such as Lipinski, Veber, CNS, lead-like, and fragment-style thresholds to identify compounds that fit a desired design space.
  • Structural risk screening: Detect PAINS, NIBR, common alerts, and other unwanted motifs before they waste downstream effort.
  • Workflow prioritization: Combine alerts, complexity metrics, chemical-group checks, and query-based logic to support hit-to-lead triage, lead optimization, and batch library cleanup.
  • Use Case: A medicinal chemist can filter a supplier library, remove unstable or promiscuous structures, and export only the molecules that meet the project’s medicinal chemistry criteria.

Quick Start

Use the medchem skill to filter the attached compound library with medicinal chemistry rules, structural alerts, and complexity thresholds, then return the molecules that pass all selected checks.

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-likeness and structural alerts?

You can filter a compound library for drug-likeness and structural alerts by applying rule-based thresholds like Lipinski and Veber alongside PAINS detection to remove problematic molecules. This process utilizes parallel batch processing to return a DataFrame of compounds that pass all selected checks.

What is the best way to prioritize molecules for hit-to-lead triage?

The best way to prioritize molecules for hit-to-lead triage is to combine structural alert removal, complexity ranking, and chemical-group detection. Applying query-based logic and Lilly demerit support enables deterministic compound selection from large screening libraries.

Can I apply custom medicinal chemistry rules to filter supplier compound libraries?

Yes, you can apply custom medicinal chemistry rules to filter supplier compound libraries. The workflow supports query-based review logic and rule evaluation to identify compounds fitting a desired design space, returning boolean masks and DataFrames for consistent screening.

Does this workflow support PAINS and NIBR structural risk screening before lead optimization?

Yes, the workflow supports PAINS and NIBR structural risk screening before lead optimization. It detects common unwanted motifs and promiscuous structures, allowing researchers to apply specific alert catalogs to prevent wasted downstream effort.

How do I use pandas and rdkit for batch library cleanup and compound filtering?

You can use pandas and rdkit for batch library cleanup by processing compound data through rule evaluations and parallel batch processing. The system outputs DataFrames and boolean masks, integrating datamol and medchem to isolate molecules meeting your medicinal chemistry criteria.