3dRNA/DNA is an automatic, fast, and high-accuracy RNA and DNA tertiary structure prediction method. It uses sequence and secondary structure information to build three dimensional structures of RNA and DNA from template segments.
The main routines for 3dRNA/DNA is:
- Break the given secondary structure into segments;
- Find the template of these segments from library, which is built from crystal or NMR structures. If the template is missing, a distance-geometry-based loop building method can be used to build the segment ab initio.
- A random template for each segment will be selected to construct the final RNA and DNA 3D structure.
- Moreover, 3dRNA/DNA is able to optimize a given structure by Simulated Annealing Monte Carlo method, and this process can further improve the prediction.