ARDA Sequences Database

The ARDA Sequences Database is a comprehensive, dynamically updated repository of all RNA sequences that have been computed and simulated on our platform.

Each time a new sequence is submitted for 3D structure prediction or evaluation, its results are automatically cataloged here. This allows researchers to explore existing data, compare results, and bypass redundant computations.

Available Data

For every sequence in the database, we provide a detailed set of metadata and simulation results.

• Sequence Metadata

  • Name: The unique identifier or descriptive name of the sequence.
  • Length: The total number of nucleotides in the sequence.
  • Date of computation: When the simulation was executed.
  • Version: The version of the ARDA platform or pipeline used.

• Simulation Parameters

  • Method: The algorithmic approach used for prediction (e.g., Bead-Springs).
  • Bead atom: The representation model used for the nucleotides.
  • Potential & Bond: Details on the physical potentials and bond constraints applied during the simulation.
  • Scoring function: The specific evaluation metric used (e.g., RASP, DFIRE, rsRNASP).
  • Computation time: The total time taken to fold and simulate the sequence.

• Results & Outputs

  • Final score: The overall quality score of the predicted structure.
  • 3D structure: Interactive visualizations and downloadable models (e.g., PDB format).
  • Folding animation: A visual playback of the sequence folding over time.
  • Trajectory: Raw simulation trajectory data.
  • Contact map: A 2D representation of nucleotide interactions and base pairings.
  • Score per folding step: Granular statistical tracking of energy and scores throughout the simulation steps.

How to Use the Database

1. Search: Use the global search bar to find specific sequences by name or attributes.
2. Analyze: Click on any sequence to open its dedicated analysis page. Here, you can interact with the 3D structure using embedded viewers.
3. Download: Export the 3D structures, trajectory files, or contact maps for use in your own local bioinformatics pipelines.