pubchem-query

Name: pubchem-query
Availability: InStock
Author: PharMolix

Query PubChem PUG REST for structures, similar compounds, and bioactivity data.

1.1k|132|Updated Apr 13, 2023

Search Tags:#retrieval #structure #bioactivity #chemistry #pubchem #similarity-search #compound-search

Ready to run

npx skills add https://github.com/PharMolix/OpenBioMed --skill pubchem-query

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: pubchem-query
Source: https://github.com/PharMolix/OpenBioMed/tree/main/skills/pubchem-query
Command: npx skills add https://github.com/PharMolix/OpenBioMed --skill pubchem-query

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

PubChem Query provides programmatic access to chemical structure retrieval, similar compound search, and bioactivity data to accelerate drug discovery workflows.

Core Features & Use Cases

Name/ID to structure: convert chemical names or identifiers to SMILES or SDF representations.
Similarity search: retrieve compounds similar to a query structure with configurable thresholds.
Bioactivity data: fetch activity information across assays, targets, and compounds.

Quick Start

Run a name-to-structure query for a compound and obtain its SMILES and related analogs.

Frequently Asked Questions about pubchem-query

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

FAQPage Schema

How do I convert a chemical name or ID to a SMILES string?▼

To convert a chemical name to a SMILES string, query PubChem using the compound name or identifier to retrieve the corresponding molecular structure representation. The tool uses PubChem PUG REST endpoints to deterministically fetch and return the requested Molecule objects and raw API responses.

Can I perform a similarity search for chemical structures with a specific threshold?▼

Yes, you can perform a similarity search for chemical structures by providing a query compound and setting a configurable similarity threshold. The search queries PubChem PUG REST endpoints to retrieve and return a list of similar compounds matching your specified criteria.

How do I fetch bioactivity data for a compound across different assays?▼

You fetch bioactivity data by querying PubChem with a compound identifier to retrieve activity information across various targets and assays. The tool applies activity filtering parameters via PUG REST endpoints and returns the specific assay and target result lists.

What is the best way to retrieve SDF representations for drug discovery workflows?▼

The best way to retrieve SDF representations is to query PubChem with your target compound name or ID to directly download the structural data file. This approach applies deterministic retrieval via PUG REST endpoints to support drug discovery workflows.

Does PubChem query return raw API responses or only parsed molecule objects?▼

PubChem query returns both parsed Molecule objects and raw API responses depending on your retrieval parameters. It implements deterministic retrieval via PUG REST endpoints to supply structural data, result lists, and the underlying raw API responses.

Are there limitations when using PubChem for bioactivity data retrieval?▼

Limitations of PubChem bioactivity retrieval include dependency on the PubChem PUG REST endpoints for response availability and the specific activity filtering parameters applied during the query. The tool returns result lists constrained by the data currently indexed in PubChem.