High-resolution comparative modeling with RosettaCM.

TitleHigh-resolution comparative modeling with RosettaCM.
Publication TypeJournal Article
Year of Publication2013
AuthorsSong, Y., DiMaio F., Yu-Ruei Wang R., Kim D., Miles C., Brunette T., Thompson J., & Baker D.
JournalStructure (London, England : 1993)
Volume21
Issue10
Pagination1735-42
Date Published2013 Oct 8
ISSN1878-4186
KeywordsPrimary Publication
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%.

DOI10.1016/j.str.2013.08.005
Custom1

http://www.ncbi.nlm.nih.gov/pubmed/24035711?dopt=Abstract

Alternate JournalStructure