Skip to main content
. Author manuscript; available in PMC: 2017 Jul 13.
Published in final edited form as: Annu Rev Biophys. 2017 Mar 15;46:227–246. doi: 10.1146/annurev-biophys-070816-033920

Table 1.

An overview of a selected set of 3D structure prediction models

Name/Reference Operation material Sampling technique Scoring function
FARNA/FARFAR(38,40) Trinucleotide fragment Monte Carlo fragment assembly Knowledge-based/full atomic force field
MC-Fold/MC-Sym(111) Nucleotide cyclic motif Las Vegas algorithm Knowledge-based scoring function
RNA2D3D(98), Assemble(69) User-defined Interactive graphical editing User-defined
RNABuilder(54) Whole structure User-defined constraints satisfaction User-defined
ModeRNA(121) Whole structure Sequence alignment Sequence similarity
Vfold(22) 2D structure based templates Template match Loop size and sequence similarity
RNAComposer(117) Stems, loops and single strands Fragment match 2D structure topology and sequence similarity
3dRNA(147) Smallest secondary elements (SSEs) SSE topology match Sequence identity
RNA123(53) Fragment and template Template match Knowledge-based force field
Graph theory approach(70, 72) Graph representation Monte Carlo graph sampling Knowledge-based energy function
DMD(46), HiRE-RNA(34), SimRNA(12) Coarse-grained beads MD/MC simulation Knowledge/physics-based force field