Gaia: automated quality assessment of protein structure models
Open Access
- 23 June 2011
- journal article
- research article
- Published by Oxford University Press (OUP) in Bioinformatics
- Vol. 27 (16), 2209-2215
- https://doi.org/10.1093/bioinformatics/btr374
Abstract
Motivation: 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. Availability and Implementation: 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. Contact:dokh@unc.edu Supplementary information: Supplementary data are available at Bioinformatics online.Keywords
This publication has 21 references indexed in Scilit:
- CAVE: A package for detection and quantitative analysis of internal cavities in a system of overlapping balls: Application to proteinsComputer Physics Communications, 2010
- Automated minimization of steric clashes in protein structuresProteins-Structure Function and Bioinformatics, 2010
- PDB_REDO: automated re-refinement of X-ray structure models in the PDBJournal of Applied Crystallography, 2009
- MolProbity: all-atom contacts and structure validation for proteins and nucleic acidsNucleic Acids Research, 2007
- Emergence of Protein Fold Families through Rational DesignPLoS Computational Biology, 2006
- Analysis of Void Volumes in Proteins and Application to Stability of the p53 Tumour Suppressor ProteinJournal of Molecular Biology, 2004
- Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand designProtein Science, 1998
- Reduced surface: An efficient way to compute molecular surfacesPeptide Science, 1996
- Rapid approximation to molecular surface area via the use of Boolean logic and look‐up tablesJournal of Computational Chemistry, 1993
- Stereochemistry of polypeptide chain configurationsJournal of Molecular Biology, 1963