DipCheck is a validation tool for the evaluation of protein backbone geometry, developed by Joana Pereira and Victor Lamzin at the EMBL Hamburg.
The tool uses a Euclidian 3D space (DipSpace) of the orthogonal descriptors of the geometry of a 5-atom dipeptide unit: CAi-1-Oi-1-CAi-Oi-CAi+1. The DipSpace database contains 1,024,000 data points derived from well-refined structures deposited in the PDB.
DipCheck classifies the geometry of a given CA (CAi) atom in four categories:
|Favoured region||98.00% of the set, DipScore above 0.243|
|Allowed region||99.80% of the set, DipScore between 0.243 and 0.033|
|Generously allowed region||99.95% of the set, DipScore between 0.033 and 0.010|
|Disallowed region||the remaining 0.05%, DipScore below 0.010|
DipCheck also classifies the overall geometry of a protein model, according to its DipScore distribution, in four categories:
|Favoured model||98.00% of a random set of protein models, Chi-score above -2.16|
|Allowed model||99.80% of a random set of protein models, Chi-score between -2.97 and -2.16|
|Generously allowed model||99.95% of a random set of protein models, Chi-score between -3.38 and -2.97|
|Outlier model||the remaining 0.05%, Chi-score below -3.38|