PubChem search

PubChem lets you search chemistry by structure, similarity, or computed property across the world's largest free compound repository — canonical SMILES, InChI, molecular weight, LogP, TPSA, and more. Reach for it when you want broad structure-based lookup or property enrichment rather than target-specific bioactivity. When you already know the target and want measured activity data, use its sibling ChEMBL instead. See what you can achieve.

PubChem integration in .bloom* platform

PubChem is NCBI's comprehensive open repository of chemical substances and compounds, aggregating data from over 1,000 contributing data sources. It is the world's largest free chemistry database. .bloom* integrates PubChem two ways: ask Ivy in chat and it runs PubChem lookups inside that turn, or open the PubChem Database Search form in the Tools panel to submit a tracked PubChem job.

Citations & Resources

Kim S, Chen J, Cheng T, Gindulyte A, He J, He S, Li Q, Shoemaker BA, Thiessen PA, Yu B, Zaslavsky L, Zhang J, Bolton EE. PubChem 2023 update. Nucleic Acids Research. 2023 Jan 6;51(D1):D1373-D1380. doi: 10.1093/nar/gkac956

Website: https://pubchem.ncbi.nlm.nih.gov

PUG REST API: https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest

Webapp search and retrieval capabilities

Search methods in .bloom*

Compound identifier lookup:

• CID search: Direct PubChem Compound ID (e.g., 2244 for aspirin)
• Name search: Chemical names, synonyms, and common identifiers
• SMILES/InChI search: Structure-based searching with automatic format detection
• CAS number lookup: Registry identifier searches

Batch processing:

• In chat: paste or upload a list of names, SMILES or CIDs; a lookup covers 10 at a time, so Ivy runs larger lists in batches
• In the form: the Batch Processing operation takes a comma-separated list of CIDs

Data retrieval and enrichment

Chemical identifiers:

• Canonical SMILES: Standardized structure representation
• Isomeric SMILES: Stereochemistry-preserving SMILES
• InChI and InChIKey: IUPAC International Chemical Identifier
• Synonyms: Multiple chemical names and identifiers
• CAS numbers: Chemical Abstracts Service registry numbers

Physicochemical properties:

• Molecular weight: Exact molecular mass calculations
• Molecular formula: Elemental composition
• LogP: Partition coefficient estimates (multiple methods)
• TPSA: Topological polar surface area
• Hydrogen bond donors/acceptors: HBD/HBA counts
• Rotatable bonds: Molecular flexibility assessment

Structural information:

• 2D coordinates: Structure visualization and editing
• 3D conformers: Multiple conformational representations
• Substructure information: Functional group annotations
• Bioassay links: Connection to biological activity data

Integration with .bloom* workflows

Compound database enrichment

Vendor search preparation:

• Standardize compound identifiers before supplier searches
• Add canonical SMILES for consistent structure handling
• Include physicochemical properties for filtering and analysis

Hit list enhancement:

• Add calculated properties to screening results
• Cross-reference structures with known compounds
• Validate compound identities from external sources

Library characterization:

• Analyze physicochemical property distributions
• Identify compound classes and structural patterns
• Generate property-based filtering criteria

Research applications

Drug discovery support:

• Access to millions of known chemical structures
• Property-based compound selection and filtering
• Integration with virtual screening workflows

Chemical informatics:

• Large-scale property calculations
• Structure-property relationship studies
• Compound library diversity analysis

Regulatory compliance:

• Access to standardized identifiers
• Reference data for safety assessments
• Cross-validation of chemical information

Webapp interface features

The PubChem Database Search form

The form in the Tools panel offers five operations, each submitted as a PubChem job you can track in your job history:

• Compound Identification: convert compound names to CIDs
• Comprehensive Search: complete compound data, optionally with molecular properties
• Fragment Library Generation: fragment-like compounds, optionally filtered by the Rule of 3 (MW ≤ 300, HBD ≤ 3, HBA ≤ 3)
• Similarity Analysis: structurally similar compounds above a threshold
• Batch Processing: a comma-separated list of CIDs

In chat

Ask Ivy for a compound lookup, property lookup, similarity search or substructure search; see search for what each takes and returns. Ivy can filter the results by property ranges and save them as CSV or SDF in the chat's code workspace.

Data quality and limitations

Coverage considerations

Data completeness:

• Not all compounds have complete property sets
• Some older entries lack modern calculated properties
• Bioassay data availability varies by compound

Data currency:

• PubChem is continuously updated
• .bloom* caches results to optimize performance
• Fresh data retrieval available on demand

Technical limitations

Rate limiting (PUG REST API):

• No more than 5 requests per second
• No more than 400 requests per minute
• No longer than 300 seconds running time per minute
• .bloom* implements intelligent caching and queuing to respect these limits

Data scope:

• Focus on small molecules and natural products
• Limited coverage of large biomolecules
• No commercial pricing or availability information

Workflow integration patterns

Compound sourcing pipeline

1. Initial search: Use PubChem to identify compounds of interest
2. Property enrichment: Add physicochemical and structural data
3. Vendor cross-check: Validate against commercial suppliers
4. Procurement planning: Generate purchase lists with standardized identifiers

Virtual screening preparation

1. Library curation: Select compounds from PubChem collections
2. Property filtering: Apply drug-like criteria and ADMET filters
3. Format standardization: Convert to consistent SMILES/InChI formats
4. Docking preparation: Feed to DiffDock or other modeling tools

Research data management

1. Data standardization: Normalize identifiers across datasets
2. Metadata enrichment: Add calculated properties and annotations
3. Quality control: Validate compound structures and data
4. Analysis preparation: Format data for statistical and cheminformatics tools

Chat Usage

Example Prompts

• "Fetch aspirin from PubChem"
• "Search PubChem for EGFR inhibitors and their properties"
• "Run a similarity search for compounds like gefitinib at 70% Tanimoto similarity"
• "Find compounds in PubChem containing a benzimidazole substructure"

Workflow Chaining

• Feeds into: ADMET-AI/ADMETLab3 (screening), DiffDock (docking), Compound Passport, AiZynthFinder (synthesis)
• Accepts from: Free-text compound names, SMILES strings from other tools

Search tools

FAQ

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