Table 3.

Some available programs for RNA tertiary-structure prediction and interactive manipulation.

Program	Input	Model	Simulation method	Description/Web page	References
Automatic prediction
iFoldRNA	Sequence	Coarse-grained three-bead model	Replica exchange, molecular dynamics	Uses discrete molecular dynamics and force fields to simulate RNA folding dynamics; http://troll.med.unc.edu/ifoldrna/	[132, 133]
FARNA (Rosetta)	Sequence, secondary structure	Coarse-grained one-bead model	Fragment assembly, Monte Carlo	Uses 3-nt fragment library, Monte Carlo simulations and a potential function to predict the structure; http://www.rosettacommons.org/manuals/archive/rosetta3.0_user_guide/index.html	[125, 127]
NAST	Secondary structure, tertiary contacts	Coarse-grained one-bead model	Molecular dynamics	Performs molecular dynamics simulations guided by a knowledge-based statistical potential function; https://simtk.org/home/nast	[131]
MC-Fold/MC-Sym	Sequence, secondary structure	Nucleotide cyclic motif	Fragment assembly, Las Vegas algorithm	Predicts RNA secondary structures using free energy minimization with structure assembled using the fragment insertion Las Vegas algorithm; http://www.major.iric.ca/MC-Pipeline/	[75]
Interactive manipulation
RNA2D3D	Secondary structure	All-atom model	Interactive manipulation	Performs molecular mechanics and dynamics, and permits insertion of coaxial stacking, and manipulation of helical elements; http://www.ccrnp.ncifcrf.gov/~bshapiro/software.html	[136]
Assemble	Database of known fragments and motifs	All-atom model	Interactive manipulation	Constructs a 3D structure using the insertion of tertiary motifs, and permits manipulation of torsion angles; http://www.bioinformatics.org/assemble/	No reference