From Protein Structure to Function with Bioinformatics.pdf

10 Integrated Servers for Structure-Informed Function Prediction 26710.3.1.6 PDBsum Structural AnalysesAlthough not strictly relevant to function prediction, a useful side effect of submittinga structure to ProFunc is that a set of PDBsum pages are also generated for it.PDBsum is a largely pictorial protein structure atlas at http://www.ebi.ac.uk/pdbsumthat performs a number of structural analyses on the submitted protein and illustratesthe results using various schematic diagrams (Laskowski et al. 2005a). A couple ofexamples are given in Fig. 10.8.10.3.2 Assessment of the Structural MethodsHow good are the structural methods at predicting protein function? The authors ofProFunc tried to answer this question by applying ProFunc to 92 models of proteinsof known function solved by the MCSG (Watson et al. 2007). In each case theProFunc predictions were adjusted to remove information from structures releasedafter the deposition of the given MCSG structure to better reflect what could havebeen predicted at the time of the structure’s deposition. The analysis showed that70% would have had their functions correctly assigned had the ProFunc server beenavailable at the time, with the correct predictions for over three-quarters of thesecoming from more than a single method.The two most successful of the structure based methods were the SSM foldcomparison method and the reverse templates. Both had a success rate of 50–60%.In fact, in most cases the two methods had the same top matches, although occasionallyone method found a correct match that the other did not. This may suggestthat, as the two methods gave such similar results, all you really need is aFig. 10.8 (continued)