Individual skill
molecular-rag
Retrieve structurally similar compounds with known properties from ChEMBL/ZINC to ground predictions and inform optimization. Based on MolRAG (Xian 2025, ACL).
backend/cli/skills/chemistry/molecular-rag/SKILL.md
Source commit a08e0ad0ad3d6448123039ee4659163eb2e35d99
What was checked
- Matches the observed repository HEAD
- Yes
- Scanner rules are current
- Yes
- Repository scan complete
- No
- Skill scan complete
- No
- Observed behavior
- Network or broad shell
- Last checked
- Nov 2, 2026
These are observations at the recorded commit, not a guarantee of safety. Review the source before running it.
Install this skill
Choose an agent in your Stack or copy a command below. Commands fetch the pinned commit and copy only this skill directory. Existing destinations are refused. Copying a command does not install anything.
An install command is unavailable: current rules, complete repository and skill scans, an eligible behavior level and a permitted license are required.
Repository context
- Repository stars (not skill ratings)
- 4,353
- Repository last updated
- Nov 6, 2026
- License
- Apache-2.0
Observed agent integration: No specific integration evidence. Standard SKILL.md installation does not imply verified compatibility.
- agent Repository topic
- ai Repository topic
- bun Repository topic
- cli Repository topic
- llm Repository topic
- ml Repository topic
- open-source Repository topic
- research Repository topic
- science Repository topic
- ai-agent Repository topic
- drug-discovery Declared skill tag
- rag Declared skill tag
- retrieval Declared skill tag
- chembl Declared skill tag
- analog-search Declared skill tag
- grounding Declared skill tag
- engineering Derived category
Files and excerpt
File metadata and permitted, redacted excerpts come from the recorded scan. Source links are pinned to that commit.
Browse files
Read excerpt
# Molecular RAG (Retrieval-Augmented Generation)
## Overview
LLMs hallucinate molecular properties. This skill grounds predictions by retrieving structurally similar compounds with experimentally measured properties from ChEMBL and ZINC. When the agent says "this compound should have good hERG safety," it can now check what happened with similar compounds in real assays.
Based on:
- **MolRAG** (Xian et al., 2025, ACL): RAG for molecular property prediction — retrieves similar compounds to ground LLM predictions
## When to Use This Skill
- **Before property prediction**: Retrieve analogs with known properties for context
- **Lead optimization**: Find what modifications worked for similar scaffolds
- **Novelty assessment**: Check if your generated molecule is truly novel or already known