title: High-quality protein backbone reconstruction from alpha carbons using Gaussian mixture models.
abstract: Coarse-grained protein structure models offer increased efficiency in structural modeling, but these must be coupled with fast and accurate methods to revert to a full-atom structure. Here, we present a novel algorithm to reconstruct mainchain models from C traces. This has been parameterized by fitting Gaussian mixture models (GMMs) to short backbone fragments centered on idealized peptide bonds. The method we have developed is statistically significantly more accurate than several competing methods, both in terms of RMSD values and dihedral angle differences. The method produced Ramachandran dihedral angle distributions that are closer to that observed in real proteins and better Phaser molecular replacement log-likelihood gains. Amino acid residue sidechain reconstruction accuracy using SCWRL4 was found to be statistically significantly correlated to backbone reconstruction accuracy. Finally, the PD2 method was found to produce significantly lower energy full-atom models using Rosetta which has implications for multiscale protein modeling using coarse-grained models. A webserver and C++ source code is freely available for noncommercial use from: http://www.sbg.bio.ic.ac.uk/phyre2/PD2_ca2main/.
authors.affiliation: Division of Molecular Biosciences, Imperial College, South Kensington Campus, London, United Kingdom.
authors.forename: Benjamin L
authors.initials: BL
authors.lastname: Moore
authors.forename: Lawrence A
authors.initials: LA
authors.lastname: Kelley
authors.forename: James
authors.initials: J
authors.lastname: Barber
authors.forename: James W
authors.initials: JW
authors.lastname: Murray
authors.forename: James T
authors.initials: JT
authors.lastname: MacDonald
mesh_terms: D000465:Algorithms; D002244:Carbon / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D011506:Proteins; D002244:Carbon
keywords: coarse-grained model; multiscale protein modeling; protein backbone; protein structure modeling; webserver