SMMRNA

SMMRNA provides a database of small-molecule ligands that target RNA to enable analysis and design of RNA-targeted modulators.

Key Features:

• Extensive Ligand Collection: Approximately 770 unique ligands are included, each with structural images of associated RNA molecules.
• Detailed Ligand Information: Per-ligand annotations include dissociation constant (Kd), inhibition constant (Ki), IC50, change in melting temperature (ΔTm), molecular weight, hydrogen bond donor and acceptor counts, XlogP, rotatable bond and aromatic ring counts, and 2D and 3D structural representations.
• Advanced Search Capabilities: Search functions include text search, advanced parameter-based queries, substructure search, and similarity-based retrieval.
• Structure Visualization and Editing: A built-in structure editor provides 3D visualization and manipulation of ligand structures.
• Chemical Similarity Analysis: Chemical similarity analysis employs substructure searches and OpenBabel-based chemical similarity fingerprints.
• Upload Facilities: Data upload supports RNA sequences and ligand records.
• Physicochemical Property Analysis: Physicochemical analyses use OpenBabel descriptors with hierarchical clustering, binning partition, and multidimensional scaling.
• 3D Conformation Database: A 3D conformation database supports structure-based and ligand-based screening.

Scientific Applications:

• Drug Discovery: Identification and optimization of small-molecule RNA-targeted therapeutics.
• Structural Biology: Analysis of ligand–RNA interactions using provided 2D and 3D structural data.
• Chemical Informatics: Comparative analysis of ligand physicochemical properties and similarity to support rational design.

Methodology:

OpenBabel descriptors and OpenBabel-based chemical similarity fingerprints, substructure searches, hierarchical clustering, binning partition, multidimensional scaling, and a 3D conformation database for structure- and ligand-based screening are used.