SimRNAweb

SimRNAweb performs RNA folding simulations and 3D structure modeling with enhanced analysis of folding trajectories and optional incorporation of experimental restraints.

Key Features:

• Coarse-grained modeling: SimRNA employs a coarse-grained model to explore RNA conformational space.
• Monte Carlo sampling: The method uses Monte Carlo sampling and statistical potentials for RNA 3D structure prediction.
• Restraint integration: SimRNAweb allows application of various hard and soft restraints, accommodating alternative structures involving canonical and noncanonical base pairs and unpaired residues.
• Experimental data incorporation: The server integrates data from chemical probing methods and supports restraints based on experimental data.
• Trajectory analysis: Enhanced analysis of folding trajectories offers advanced clustering options and multiple analyses of generated trajectories.
• Performance optimization: The server version introduces performance optimizations and extended control over simulations and processing of results.

Scientific Applications:

• RNA 3D structure prediction: SimRNAweb predicts RNA three-dimensional structures, recognized for accuracy in RNA-Puzzles and CASP competitions.
• Folding trajectory analysis: The server analyzes RNA folding trajectories with advanced clustering and multiple analysis options.
• Experimentally guided modeling: SimRNAweb incorporates spatial restraints and experimental data to guide RNA conformational exploration.

Methodology:

SimRNA employs a coarse-grained model, Monte Carlo sampling and statistical potentials to explore RNA conformational space, optionally guided by spatial restraints.