RNABuilde
r is a program for RNA 3D structure modeling. It allows the user to specify a set of constraints for base pairing and stacking, distance restraints, rigidifying portions of the molecule, and many more. In practice, these can be combined to thread a RNA chain to one or more structural templates, and relax the structure of elements not represented in the template. Given a description of the structural interactions (the more knowledge, the better), RNABuilder is able to construct an RNA model. There is however a chance that the RNA chain will get tangled during the simulation (the minimization gets caught in local minima) – the user may resolve this with RNABuilder’s simulated annealing and potential rescaling features.
RNABuilder was successfully used to build a comparative model for the Azoarcus group I intron using two template structures (from the Twort phage and Tetrahymena).
Internally, RNABuilder uses the Simbody/Molmodel [1] internal coordinate library to represent a full-atomic and a coarse-grained model in parallel. By default, no forces act on the atoms unless constraints are specified. Forces are resolved by a harmonic potential that becomes inverse at distances higher than a cutoff value. The user can specify the desired bond mobility; this means that residues or entire domains can be rigidified for cost savings or other modeling reasons. By default most bonds permit torsional rotations but not stretching or angle bending.
RNABuilder can be found on: http://www.simtk.org
[1] J.P. Schmidt, et al., Proceedings of the IEEE, 2008, 96, 1266-1280.
[2] Flores, S.C., Wan, Y., Russell, R. and Altman, R.B. Predicting RNA structure by multiple template homology modeling. Pac Symp Biocomput, 216ff.
(c) 2011 Kristian Rother and Samuel Flores
