High-resolution comparative modeling with RosettaCM

Structure. 2013 Oct 8;21(10):1735-42. doi: 10.1016/j.str.2013.08.005. Epub 2013 Sep 12.


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%.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural

MeSH terms

  • Computer Simulation*
  • Models, Molecular*
  • Monte Carlo Method
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Proteins / chemistry
  • Software*
  • Structural Homology, Protein


  • Proteins