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High-resolution comparative modeling with RosettaCM.

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%.

SUBMITTER: Song Y

PROVIDER: S-EPMC3811137 | biostudies-literature | 2013 Oct

REPOSITORIES: biostudies-literature

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High-resolution comparative modeling with RosettaCM.

Song Yifan Y DiMaio Frank F Wang Ray Yu-Ruei RY Kim David D Miles Chris C Brunette Tj T Thompson James J Baker David D

Structure (London, England : 1993) 20130912 10

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 m ...[more]

PMID: 24035711

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