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

High-resolution comparative modeling with RosettaCM.

Author information

1
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.

Abstract

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%.

PMID:
24035711
PMCID:
PMC3811137
DOI:
10.1016/j.str.2013.08.005
[Indexed for MEDLINE]
Free PMC Article

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