R-SIM

RNA-Small Molecule Interaction Miner (R-SIM): Database of Experimentally Validated RNA–Small Molecule Interactions

RNA-Small Molecule Interaction Miner (R-SIM) compiles experimentally validated RNA–small molecule interactions to support RNA-targeted drug discovery and analysis of target selectivity.

Key Features:

• Curated Interaction Database: Stores experimentally validated RNA–small molecule interaction records.
• RNA Target Annotation: Provides RNA sequence, secondary or tertiary structure, and functional classification.
• Small Molecule Characterization: Includes physicochemical properties of interacting small molecules.
• Binding Affinity Data: Reports quantitative binding affinity values with associated experimental conditions.
• Structural Complex Data: Contains three-dimensional structures of RNA–small molecule complexes from experimental determination or computational modeling.
• Literature Referencing: Links each entry to primary literature sources.

Scientific Applications:

• Target Identification: Enables identification of RNA targets based on experimentally measured binding affinities.
• Structure-Guided Drug Design: Supports rational design of RNA-targeting small molecules using structural and physicochemical data.
• RNA-Targeted Therapeutic Development: Facilitates development of therapeutics targeting RNA in diseases including cancers, bacterial infections, viral infections, and neurodegenerative disorders.

Methodology:

R-SIM is constructed through manual curation of experimentally validated RNA–small molecule interaction data, including validation and classification of RNA sequences and structures, extraction of physicochemical properties of small molecules, and compilation of binding affinity measurements and structural complex information from primary literature and computational modeling studies.