Towards a better measure of protein 3D model quality

Advances in protein three-dimensional structure prediction depend strongly on the ability to measure the quality of a protein model. One of the best single measures of the model quality is the area under the graph of the so-called “GDT function” that assigns to each distance cutoff θ the percentage of residues in the model structure that can be superimposed at distance ≤ θ from the corresponding residues in the experimental structure. In lieu of a method capable of computing this measure, researchers often resort to its approximation GDTTS. In this short paper we present the first theoretical framework for the development of an algorithm capable of computing near-optimal estimates of the area under the GDT curve of a protein model in polynomial time.