SphereGrinder - reference structure-based tool for quality assessment of protein structural models

Abstract

3D protein structure prediction is of significant interest in the biological research community. Nowadays, one can find many methodologies that can lead to model protein structures, and for that reason the plausible assessment of the quality of protein structural models has fundamental impact on the progress of structural bioinformatics. Here, we present SphereGrinder, a novel computational tool devoted to evaluation of protein 3D models according to the reference structure that gives an opportunity to proceed with structural analysis from atomic to the whole molecule level of accuracy. Proposed tool is capable of handling large predicted models set is designed and used for protein structure prediction in CASP (Critical Assessment of Techniques for Protein Structure Prediction) experiment to complement and add value to the traditional protein structure quality assessment by the global distance test and related scores. SphereGrinder is a user-friendly software that allows the comprehensive quality inspection conducted between the set of predicted protein models and the reference structure. It is implemented as an online application available for free use by all academic users at the URL http://spheregrinder.cs.put.poznan.pl.