PubChem

PubChem provides a public repository of biological activity data for small molecules and small interfering RNAs (siRNAs), storing assay descriptions and experimental bioactivity outcomes to enable analysis of compound activities and target relationships.

Key Features:

• Bioassay records: Contains assay descriptions, summaries, and detailed test outcomes for small molecules and siRNAs.
• Molecular target linkage: Assay records are linked to molecular targets, including protein and gene annotations, where possible.
• Cross-references to NCBI: Assay records are cross-referenced with other NCBI database entries.
• Related BioAssays identification: Facilitates identification of Related BioAssays via analysis of assay target relationships and activity profiles.
• Programmatic access and Entrez indexing: Integrated with the NCBI Entrez information retrieval system and provides programmatic access for data retrieval and analysis.
• Analytical capabilities: Supports aggregation, comparison, and analysis of biological test results across assays and compounds.
• Data scale: Contains over 500,000 assay protocol descriptions, approximately 5,000 protein targets, 30,000 gene targets, and more than 130 million recorded bioactivity outcomes.

Scientific Applications:

• Drug discovery: Aggregated bioactivity data support identification and optimization of small-molecule leads.
• Molecular biology: Enables analysis of siRNA biological activity and gene-targeted assay results.
• Target characterization: Supports characterization and annotation of protein and gene targets through linked assay data.
• Bioactivity profiling and comparative analysis: Facilitates profiling and comparison of compound activity signatures across assays.
• Assay protocol reference: Provides extensive assay protocol descriptions for method reference and comparison.

Methodology:

Records are linked to molecular targets and cross-referenced with other NCBI database entries, indexed in the NCBI Entrez system, and analyzed by comparing assay target relationships and activity profiles with programmatic data retrieval.