LigandRNA

LigandRNA predicts and scores three-dimensional poses of small-molecule ligands bound to RNA structures, focusing on riboswitches to identify potential binding sites and rank ligand–RNA interactions.

Key Features:

• Scoring and ranking of 3D poses: Scores and ranks three-dimensional ligand poses docked to RNA structures.
• Knowledge-based scoring function: Employs a knowledge-based scoring function to evaluate ligand–RNA interactions.
• Binding site prediction: Predicts potential small-molecule binding sites on RNA structures.
• Riboswitch focus: Targets riboswitches and mRNA regulatory regions that undergo structural changes upon ligand binding.
• Ligand and metal ion interactions: Accounts for interactions with small-molecule ligands and metal ions.

Scientific Applications:

• Drug design and molecular engineering: Ranks candidate ligands for modulating riboswitch activity in drug discovery and molecular engineering efforts.
• Riboswitch functional studies: Facilitates structural and functional studies of riboswitches and other RNA-based regulatory elements.
• Prioritization for experimental validation: Provides theoretical prioritization of binding sites and ligands to guide experimental validation.

Methodology:

Uses a knowledge-based scoring function to score and rank three-dimensional ligand poses and predict binding sites on RNA structures.