TBI

TBI predicts ion effects on RNA structures, including multivalent ions such as Mg²⁺, by quantifying electrostatic free energy, ion binding fractions and modes, and ion correlation and fluctuation effects to inform RNA folding and stability.

Key Features:

• Electrostatic Free Energy Prediction: Calculates total electrostatic free energy of ion binding for RNA structures provided in PDB format and decomposes it into component contributions.
• Ion Binding Modes and Fractions: Predicts average ion binding fractions and identifies the most probable ion binding modes on the RNA surface.
• Accounting for Ion Correlation Effects: Explicitly incorporates ion correlation effects that arise for multivalent ions near the RNA surface.
• Ion Distribution Fluctuation Analysis: Accounts for fluctuations in ion distribution to capture variability in ion-mediated electrostatic interactions.

Scientific Applications:

• RNA Folding Stability: Analyzes ion-dependent changes in electrostatic free energy to assess RNA tertiary structure stability under varying ionic conditions.
• Ion Uptake During Folding: Provides insights into ion uptake and incorporation during RNA folding processes.
• Energetic Component Interplay: Enables exploration of interactions among different energetic components governing RNA folding.

Methodology:

Implements a tightly bound ion model that integrates ion correlation and fluctuation effects to represent the electrostatic environment of RNA in salt solutions with specified ion concentrations.