The basic metrics of RNA 3D structure comparison include:

  • Root Mean Square Deviation (RMSD)
  • P value
  • Deformation Index
  • Interaction Network fidelity
    • this metric can be measured by different types of contacts, including:
    • all contacts
    • Watson-Crick interaction
    • non-Waston-Crick interaction
    • stacking

All of these metrics have been implemented in Basic Assess Metrics (author: Chichau)