RNA 3D Structure Resources

• Protein Data Bank (PDB) database
• Nucleic Acid Database (NDB)
• Protein-RNA Docking Benchmark

RNA tertiary structure prediction methods

• 3dRNA
• Vfold3D
• iFoldRNA
• RNAComposer
• SimRNA

Molecular Dynamics

• AMBER
• CHARMM
• GROMACS

Molecular Docking

• DOCK
• ZDOCK
• AutoDock
• 3dRPC
• HDOCK

Molecular Visualization/Analysis

• PyMol
• Chimera
• Visual Molecular Dynamics (VMD)