How do I install the Chem Similarity Search skill?

Run npx skillmds@latest add learningmatter-mit/chem-similarity-search in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Chem Similarity Search safe to use?

This skill has not completed SkillMD's automated safety review yet. Independent scanners report: SkillSpector: PASS, Skill Scanner: PASS. Capability flags: executes scripts, makes network calls. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Chem Similarity Search?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Chem Similarity Search free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Chem Similarity Search?

learningmatter-mit (@learningmatter-mit) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Chem Similarity Search by learningmatter-mit

Name: Chem Similarity Search
Rating: 4.2 (5 reviews)
Author: learningmatter-mit

File contents

Chemical Similarity Search

Goal

To programmatically find chemical analogs, alternative precursors, and structurally similar compounds for a given target molecule using PubChem's "fastsimilarity_2d" endpoint. The skill retrieves lists of similar compounds ranked by sequence alignment of their 2D molecular fingerprints, providing CIDs, molecular weights, formulas, and SMILES strings.

Instructions

1. Search by SMILES String

Search for similar compounds by providing the canonical or isomeric SMILES. Adjust the --threshold (similarity cutoff 0-100, default is 95) to widen or narrow the search radius. Higher threshold equals higher similarity. Adjust --max_records to limit the output length.

# Env: base-agent
python .agents/skills/chem-similarity-search/scripts/similarity_search.py \
  --smiles "CC(=O)Oc1ccccc1C(=O)O" \
  --threshold 95 \
  --max_records 5 \
  --outdir research/aspirin_similar \
  --output aspirin_similar.json

2. Search by PubChem CID

Search directly using an exact compound's CID. This avoids translation steps for SMILES parsing.

# Env: base-agent
python .agents/skills/chem-similarity-search/scripts/similarity_search.py \
  --cid 2244 \
  --threshold 90 \
  --max_records 10 \
  --outdir research/aspirin_similar \
  --output cid_2244_similar.json

Examples

We can test extracting highly similar analogs (Threshold 95) for Aspirin (CID: 2244 or SMILES: CC(=O)Oc1ccccc1C(=O)O).

# Env: base-agent
python .agents/skills/chem-similarity-search/scripts/similarity_search.py \
  --cid 2244 \
  --threshold 95 \
  --max_records 5 \
  --outdir .agents/skills/chem-similarity-search/examples/aspirin_analogs \
  --output aspirin_analogs.json

Constraints

Rate Limiting: PubChem PUG REST API enforces per-user throttling limits. Heavy bursts will result in HTTP 503 Server Busy errors. The script implements an exponential backoff retry mechanism.
2D Similarity: Uses exact structural bit-vector fingerprints. Stereochemical and 3D properties do not strongly affect the score.
Network: Internet access is required.

Author: Bowen Deng Contact: GitHub @learningmatter-mit

---name: chem-similarity-searchdescription: Find structurally similar chemical compounds using PubChem's 2D fast similarity engine via the PUG-REST API.---# Chemical Similarity Search## GoalTo programmatically find chemical analogs, alternative precursors, and structurally similar compounds for a given target molecule using PubChem's "fastsimilarity_2d" endpoint. The skill retrieves lists of similar compounds ranked by sequence alignment of their 2D molecular fingerprints, providing CIDs, molecular weights, formulas, and SMILES strings.## Instructions### 1. Search by SMILES StringSearch for similar compounds by providing the canonical or isomeric SMILES.Adjust the `--threshold` (similarity cutoff 0-100, default is 95) to widen or narrow the search radius. Higher threshold equals higher similarity.Adjust `--max_records` to limit the output length.```bash# Env: base-agentpython .agents/skills/chem-similarity-search/scripts/similarity_search.py \ --smiles "CC(=O)Oc1ccccc1C(=O)O" \ --threshold 95 \ --max_records 5 \ --outdir research/aspirin_similar \ --output aspirin_similar.json```### 2. Search by PubChem CIDSearch directly using an exact compound's CID. This avoids translation steps for SMILES parsing.```bash# Env: base-agentpython .agents/skills/chem-similarity-search/scripts/similarity_search.py \ --cid 2244 \ --threshold 90 \ --max_records 10 \ --outdir research/aspirin_similar \ --output cid_2244_similar.json```## ExamplesWe can test extracting highly similar analogs (Threshold 95) for Aspirin (CID: 2244 or SMILES: `CC(=O)Oc1ccccc1C(=O)O`).```bash# Env: base-agentpython .agents/skills/chem-similarity-search/scripts/similarity_search.py \ --cid 2244 \ --threshold 95 \ --max_records 5 \ --outdir .agents/skills/chem-similarity-search/examples/aspirin_analogs \ --output aspirin_analogs.json```## Constraints- **Rate Limiting**: PubChem PUG REST API enforces per-user throttling limits. Heavy bursts will result in `HTTP 503 Server Busy` errors. The script implements an exponential backoff retry mechanism.- **2D Similarity**: Uses exact structural bit-vector fingerprints. Stereochemical and 3D properties do not strongly affect the score.- **Network**: Internet access is required.------**Author:** Bowen Deng**Contact:** [GitHub @learningmatter-mit](https://github.com/learningmatter-mit)

Frequently asked questions

Chem Similarity Search