title: Gaia: automated quality assessment of protein structure models.
abstract: BACKGROUND
  Increasing use of structural modeling for understanding structure-function relationships in proteins has led to the need to ensure that the protein models being used are of acceptable quality. Quality of a given protein structure can be assessed by comparing various intrinsic structural properties of the protein to those observed in high-resolution protein structures.
  
  
  RESULTS
  In this study, we present tools to compare a given structure to high-resolution crystal structures. We assess packing by calculating the total void volume, the percentage of unsatisfied hydrogen bonds, the number of steric clashes and the scaling of the accessible surface area. We assess covalent geometry by determining bond lengths, angles, dihedrals and rotamers. The statistical parameters for the above measures, obtained from high-resolution crystal structures enable us to provide a quality-score that points to specific areas where a given protein structural model needs improvement.
  
  
  METHODS
  We provide these tools that appraise protein structures in the form of a web server Gaia (http://chiron.dokhlab.org). Gaia evaluates the packing and covalent geometry of a given protein structure and provides quantitative comparison of the given structure to high-resolution crystal structures.
  
  
  BACKGROUND
  dokh@unc.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, NC 27599-7260, USA.
authors.forename: Pradeep
authors.initials: P
authors.lastname: Kota
authors.forename: Feng
authors.initials: F
authors.lastname: Ding
authors.forename: Srinivas
authors.initials: S
authors.lastname: Ramachandran
authors.forename: Nikolay V
authors.initials: NV
authors.lastname: Dokholyan
mesh_terms: D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry; D012984:Software
chemical_list: D011506:Proteins