Structural biologists interpretation

Still structure prediction is an unsolved problem and the methods available are rough and heuristic. The outcome of predictions is not easily interpreted by the non-specialist and can easily be over-interpreted by biologists if taken too seriously. The computation of suitable p-values to allow for a straightforward judgment of the respective prediction remains problematic for many methods and parameter settings. In addition, models derived from similarities on the fold level often simply are not as structurally similar as one could hope for, i.e. not very usable for detailed structural analysis. Variations and differences apart from conserved structural cores have to be expected frequently even for highly significant structural predictions. 

In 1965, Jacques Monod stated in his Nobel lecture that the ambition of molecular biology is to interpret the essential properties of organisms in terms of molecular structures [1]. Similarly, it would be no exaggeration to say that most computational biologists naturally believe that the ambition of computational molecular biology is to interpret the essential functions of organisms in terms of molecular dynamics. ... 

Abstract. Most visualization systems fail to convey uncertainty within data. To provide a way to show uncertainty in similar hierarchies, we interpreted the differences between two tree structures as uncertainty. We developed a new interactive visualization system called CandidTree that merges two trees into one and visualizes two types of structural uncertainty location and sub-tree structure uncertainty. We conducted a usability study to identify major usability issues and evaluate how our system works. Another qualitative user study was conducted to see if biologists, who regularly work with hierarchically organized names, are able to use CandidTree to complete tree-comparison tasks. We also assessed the uncertainty metric we used. 

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