![]() ![]() We name our dynamic free-energy diagrams dFEDs.Ĭopyright © 2014 Elsevier Ltd. Of note, the diagrams describe free energy landscapes thus, they can be quantified. ![]() We create templates for function classification and suggest that they can extend signaling pathway maps. "Function diagrams" are important: they can combine diverse biochemical data to visually distinguish among activation (or recruitment) mechanisms and tag proteins in cellular networks, clarifying their mechanism at a glance. If the number of lists is lower than 7 it will also produce a graphical output in the form of a venn/Euler diagram. It will generate a textual output indicating which elements are in each intersection or are unique to a certain list. The funnel shape around the proteins' native states can describe mechanisms of upstream signal integration and downstream response. With this tool you can calculate the intersection (s) of list of elements. Here, we show that simple funnel drawings can capture and usefully portray proteins by their cellular triggering mechanism. Capturing function is challenging, since activation involves triggered dynamic shifts between ON and OFF states. Both have been extraordinarily successful in capturing complex static features of sequences and structures. Two common examples are sequence logos and ribbon diagrams. Simplified representations can be powerful. ![]()
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