title: A three dimensional visualisation approach to protein heavy-atom structure reconstruction.
abstract: BACKGROUND
  A commonly recurring problem in structural protein studies, is the determination of all heavy atom positions from the knowledge of the central α-carbon coordinates.
  
  
  RESULTS
  We employ advances in virtual reality to address the problem. The outcome is a 3D visualisation based technique where all the heavy backbone and side chain atoms are treated on equal footing, in terms of the Cα coordinates. Each heavy atom is visualised on the surfaces of a different two-sphere, that is centered at another heavy backbone and side chain atoms. In particular, the rotamers are visible as clusters, that display a clear and strong dependence on the underlying backbone secondary structure.
  
  
  CONCLUSIONS
  We demonstrate that there is a clear interdependence between rotameric states and secondary structure. Our method easily detects those atoms in a crystallographic protein structure which are either outliers or have been likely misplaced, possibly due to radiation damage. Our approach forms a basis for the development of a new generation, visualization based side chain construction, validation and refinement tools. The heavy atom positions are identified in a manner which accounts for the secondary structure environment, leading to improved accuracy.
authors.affiliation: Department of Physics and Astronomy, Uppsala University, Uppsala, Sweden. xubiaopeng@gmail.com.
authors.forename: Xubiao
authors.initials: X
authors.lastname: Peng
authors.affiliation: Department of Physics and Astronomy, Uppsala University, Uppsala, Sweden. achenani@gmail.com.
authors.forename: Alireza
authors.initials: A
authors.lastname: Chenani
authors.affiliation: Department of Physics and Astronomy, Uppsala University, Uppsala, Sweden. hushuangwei@gmail.com.
authors.forename: Shuangwei
authors.initials: S
authors.lastname: Hu
authors.affiliation: Department of Biomedicine, Faculty of Medicine and Dentistry, University of Bergen, Jonas Lies Vei 91, NO-5009, Bergen, Norway. ahan.zhou@gmail.com.
authors.forename: Yifan
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: Department of Physics and Astronomy, Uppsala University, Uppsala, Sweden. Antti.Niemi@physics.uu.se.|Laboratoire de Mathematiques et Physique Theorique CNRS UMR 6083, Fédération Denis Poisson, Université de Tours, Parc de Grandmont, F37200, Tours, France. Antti.Niemi@physics.uu.se.
authors.forename: Antti J
authors.initials: AJ
authors.lastname: Niemi
mesh_terms: D003198:Computer Simulation; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins