Reaction Explorer ManualUpon starting Reaction Explorer you will be greeted by three windows: Compound, Reaction and Graph (labelled initially as "Reaction Network"). The name of the database server to which Reaction Explorer is connected is displayed at the bottom of the Compounds window. Should no database be found at startup, the application will quit.
Compound SearchEnter the name of a starting compound into the text box of the Compound Window and press Return or click the "Enter" button. The reaction database contains a large list of compound synonyms, and space and hyphen distinctions are ignored. Inexact searching is enabled by default; check the "Use exact search" checkbox to disable this.
Exact searches may be made inexact by the use of the wildcard character, "*".
The primary terms for compounds matching the user-entered chemical name are shown in the bottom half of the Compounds window. In the case of exact searches, more than one primary term will be returned if those terms share the search term as a common synonym.
Reaction SearchClick on a compound name to search for all reactions involving the compound identifier associated with that name. The compound name will be added to the Reaction Network window. The search results are shown in the upper half of the Reactions window. Select a reaction by clicking on it and the possible products will be shown in the lower pane.
Click on a product to add that compound to the graph; a line representing the reaction will be drawn between both it and the chosen substrate. At the same time, the Reaction window will be updated to show all reactions involving the selected product. Continue adding compounds and reactions to the Reaction Network window as desired. The History window (available from the Window menu) shows all of the reactions that have been added to the graph since the start of the session.
It should be noted that certain compounds are not allowed to be used as nodes on the graph, due to the number of reactions in which they participate. For example, neither "H+" nor "H2O" will be added as nodes to the network graph. Likewise, common cofactor pairs are not allowed as substrate-product pairs; for example, NADH/NAD+ and ATP/ADP. This is to prevent linkages from, e.g., D-glucose to ADP in the reaction catalysed by glucokinase
Click here to view complete list of all such "blacklisted" compounds and common cofactor pairs.
Reaction Network GraphClick and drag on the name of a compound appearing in the Reaction Network window to move it. Holding down the Alt (Option) key while dragging a compound's name will move the entire graph.
Files and PrintingUse the File menu to save, load or print graphs. Some ready-made metabolic network graphs can be found in the Example Graphs folder.