Assessing the quality of protein models is essential for ranking models, refining models and using models (Cheng, 2008).
Progress in the field of protein three-dimensional structure prediction depends on the development of new and improved algorithms for measuring the quality of protein models.
TM-align TM-align is another popular protein structure alignment program, widely used in many applications, in particular for assessing the quality of protein models generated by comparative modeling or abinitio techniques.
TM-align is another popular protein structure alignment program, widely used in many applications, in particular for assessing the quality of protein models generated by comparative modeling or abinitio techniques.
Results: In this work, we present a new absolute measure for the quality of protein models, which provides an estimate of the 'degree of nativeness' of the structural features observed in a model and describes the likelihood that a given model is of comparable quality to experimental structures.
Therefore, the predicted solvent accessibility has been widely utilized for detection as well as threading of remote homologous proteins [ 21– 23] and quality assessment of protein models [ 24, 25].
This specific, but highly relevant, important aspect of protein model quality assessment has received only little attention in recent years (Heim and Li, 2012; Ray et al., 2010).
Perhaps the best descriptor of the quality of a protein model is the GDT function that maps each distance cutoff θ to the number of atoms in the protein model that can be fit under the distance θ from the corresponding atoms in the experimentally determined structure.
The graph of a GDT function provides a valuable insight into the quality of a protein model (Fig. 1).
The quality of the protein model generated was validated by using the PROCHECK program as described previously.
