Query PubChem PUG REST for structures, similar compounds, and bioactivity data.
npx skills add https://github.com/PharMolix/OpenBioMed --skill pubchem-query
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
PubChem Query provides programmatic access to chemical structure retrieval, similar compound search, and bioactivity data to accelerate drug discovery workflows.
Run a name-to-structure query for a compound and obtain its SMILES and related analogs.
High-intent search queries and answers about installing and using this skill.
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.
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.
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.
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.
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.
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.
google-deepmindResolve chemical names, InChI, or SMILES into PubChem CIDs and retrieve identifiers, properties, safety text, and pharmacology annotations.
InternSciencePredicts ADMET properties for batches of molecules from SMILES strings or files.
jasrajtulsiParse and analyze molecular structures with RDKit for cheminformatics workflows.
LeonChaoXRetrieve PubChem compound properties, synonyms, and bioactivity data by identifier or structure.
