General description
Validation of protein tertiary structure models is a very important issue in structural biology. The presented method meets this challenge. The SphereGrinder provides the research community with a freely available and easy to use software tool for comprehensive quality inspection conducted between the set of predicted protein models and the reference structure. It is designed to complement and add value to the traditional protein structure quality assessment by the global distance test (GDT) and related scores. It is platform independent Java software that provides an user-friendly environment, where user can with only a few clicks localize and analyze an interesting structural motif of current model, represented as a sphere built around selected amino-acid residue with particular sphere radius defined by researcher. The SphereGrinder equipped with an advanced visualization features (e.g. 2d map, 3d landscape) allows users to identify correct and incorrect structural motives from protein structure predictions taking into consideration different levels of accuracy. It may be used to evaluate structures from different points of view, to observe prediction diffculty and to identify promising predictions even if they seem to be inappropriate. The proposed tool could also support homology modeling of protein structure prediction. It was applied to all targets from CASP9 contest (e.g. the analysis of T0522-D1 target). The SphereGrinder was implemented in such a way that is capable of handling large predicted models set, a growing requirement in the CASP experiment.