Empath - metabolic pathway chart

Empath is a Cabinet database of metabolic pathways that models a metabolic pathway chart. It initially models the Boehringer Mannheim wall chart [35] but other pathway layouts are possible. It currently includes 1462 steps (metabolic reactions). The Empath database consists of more than 8000 live objects. Every object has an exact geometric location, that is, x, y coordinate, which is optionally indicated by visible hotspots. The chart is clickable everywhere and the image recenters itself around the selected point. The current object is the one closest to the center of the image and is identified by a bull s eye. A summary of the object is given (e.g., its structure, EC number, SMILES, reaction stoichiometry, etc.). Empath provides navigational features such as zoom in/out, wider, thinner, taller and shorter. 

Empath maintains ten object classes. Landmarks indicate a general area of the chart where a particular metabolism occurs. Compounds are primary reactants and products. Cofactors are additional reactants and products that usually drive steps energetically. Enzymes are the primary catalysts of steps most of them have an associated EC number. Agents are secondary catalysts, usually metal ions. Regulators are substances that enhance or suppress a particular reaction. Steps are reactions that include aU of the above object types. Pathways are sequences of life essential steps or steps that occur across all species. Diseases as well as Notes are associated with steps. Abbreviations are a separate category for abbreviated names on the chart and have a link to the area of primary synthesis. 

A fingerprint similarity search is available within Empath by selecting similar in the summary of objects that includes structures. The related button finds similar structures in other Cabinet databases. 

A directed graph search is available where compounds are nodes and metabolic steps are edges. The server finds the shortest allowable path between one node and another. One can limit the search to steps that occur in a certain kingdom and can also choose to display only pathways visually connected on the metabolic pathway chart. There are thousands of connections that are not drawn on the chart but can be found by using this search. 

Empath provides a view of a reaction in the context of metabolic pathways. As such, it serves as an index for other Cabinet databases. 

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In our example, EC book and Empath find an exact match to HMG-CoA reductase. The Empath link shows the metabolic step that the enzyme catalyzes (Figure 10.5 [50]). The reaction is between S-3-hydroxy-3-methylglutaryl-CoA and Mevalonate. The step summary on the right side of the chart image shows activation and regulation of the enzyme, its biological scope, direction, reversibility and stoichiometry. A pathway search... 

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See also in sourсe #XX -- [ ]

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