1. Department of Fundamental Research, National Institute of Biomedical Innovation, 7-6-8 Saito-asagi, Ibaraki-shi, Osaka, Japan.
Background: Prediction of protein tertiary and quaternary structures helps us to understand protein functionality. While tertiary structure prediction techniques have been much improved over the last two decades, quaternary structure (homo-oligomer) prediction has not been paid much attention to.
Results: We show the results of the assessment of our simple auto server prediction and manual prediction of protein quaternary structure from its amino acid sequence based on templates. They were tested in the 9th Critical Assessment of Protein Structure Prediction (CASP9) experiment. CASP experiments are the only true blind test for protein tertiary and quatenary structure prediction from amino acid sequence alone and therefore they are the most severe tests in the field of protein stucture prediction. Our simple auto server prediction could generate successful models for 14 out of 58 targets. Human experts could generate successful models for 11 out of 16 targets and most of them were better than those by our auto server.
Conclusions: The results show the efficiency of our template-based protein quaternary structure prediction approaches and provide useful information for improvement of the accuracy of template-based quaternary structure prediction.