title: 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%.
authors.affiliation: Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
authors.forename: Yifan
authors.initials: Y
authors.lastname: Song
authors.forename: Frank
authors.initials: F
authors.lastname: DiMaio
authors.forename: Ray Yu-Ruei
authors.initials: RY
authors.lastname: Wang
authors.forename: David
authors.initials: D
authors.lastname: Kim
authors.forename: Chris
authors.initials: C
authors.lastname: Miles
authors.forename: Tj
authors.initials: T
authors.lastname: Brunette
authors.forename: James
authors.initials: J
authors.lastname: Thompson
authors.forename: David
authors.initials: D
authors.lastname: Baker
mesh_terms: D003198:Computer Simulation; D008958:Models, Molecular; D009010:Monte Carlo Method; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry; D012984:Software; D040681:Structural Homology, Protein
chemical_list: D011506:Proteins
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