High-resolution comparative modeling with RosettaCM.
|Title||High-resolution comparative modeling with RosettaCM.|
|Publication Type||Journal Article|
|Year of Publication||2013|
|Authors||Song, Y., DiMaio F., Yu-Ruei Wang R., Kim D., Miles C., Brunette T., Thompson J., & Baker D.|
|Journal||Structure (London, England : 1993)|
|Date Published||2013 Oct 8|
We describe an improved method for comparative modeling, RosettaCM, which optimizes a physically realistic all-atom energy function over the conformational space defined by homologous structures. Given a set of sequence alignments, RosettaCM assembles topologies by recombining aligned segments in Cartesian space and building unaligned regions de novo in torsion space. The junctions between segments are regularized using a loop closure method combining fragment superposition with gradient-based minimization. The energies of the resulting models are optimized by all-atom refinement, and the most representative low-energy model is selected. The CASP10 experiment suggests that RosettaCM yields models with more accurate side-chain and backbone conformations than other methods when the sequence identity to the templates is greater than ∼15%.