ePathway Database is the part of ePath3D which offers a 3D pathway illustration tool and Hundreds of Pre-made Pathways which are linked to the eProtein Database. Both, the ePathway Database and eProtein Database are part of the ePath3D software, there are no additional charges for these database.

Getting Started

Opening Screen Shots of ePathway

The below screenshot displays the opening screen of ePathway. The current drawing window is blank, you can select from any of the drawing item folders or premade pathways folder which are shown at the left side of the screen; you can select items from these folder to start drawing a pathway.



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Premade Pathways

ePathway contains hundreds of pre-made signal transduction and metabolic pathways. All pathways have been created by the Protein Lounge biology team and are well referenced. The premade pathways are located in the folder at the left labelled "Pre-made Pathways" and also in the "Pathways Favorites" icon found in the top tool bar.



Selecting Pathway from the Pre-made folder

In the Pre-made pathways folder you can search by pathway name, view pathway by alphabetical order or by category. Once you find the pathway of interest, just double click on it and it will open in the drawing window. You can further modify the pre-made pathway if required.



Selecting Pathways from the Pathway Favorites



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How to Draw a Pathway

In addition to modifying pre-made pathways, you can draw a pathway from scratch by selecting from the biological membranes, protein images and other accessory items from the folders at the left.

Membranes Folder

This folder contain the type of cellular membranes which you would require to draw a pathway.



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How to Use Membranes

There are three types of membranes

1. Bi-point Membrane: contains two flexi-points, it is easier to use, but it allows for less flexibility, only single curves are possible.

2. Multipoint Membrane: contains many points, it is a little more difficult to use, but allows for much more flexibility, you can     make several curves on a single membrane.

3. Circular Membrane: these membranes do not have any flexi-points, they are just circular and can be expanded or reduced.

Bi-point Membranes

To place a Bi-point membrane, click on the membrane type in the Membranes folder shown at the left of the screenshot. This type of membrane can be used to make a simple pathway, which does not require too much detail in the membrane folding. There are two flexi-points at each end of the membrane which allow you to bend it, as shown below. This type of membrane is very easy to use and is recommend for someone who is making a quick and simple pathway.



Multipoint Membranes

To place a Multipoint membrane, click on the membrane type in the Membranes folder shown at the left of the screenshot. This type of membrane allows for much more flexibility in curvature. There are more then 20 points placed along the membrane, which allow you to better curve the membrane to produce such things, as vesicle endo/exocytosis. Important: you can not simple click on the membrane with the point, to produce the curves you must use the pencil tool (located in the top Tool Bar or Control Panel, circled in red below). Click on the Pencil Tool, then click on the membrane and stretch the points. The pointer tool can be used to move and stretch the membrane.

Circular Membrane

These membranes do not have any flexi-points, they are just circular and can be expanded or reduced. The circular membranes can be used for vesicles or circular cell shape structures.

Other Types of Membranes

The membrane folder also contains Plant Membranes, Gram Positive and Gram Negative Bacterial Membranes. All of these membranes are Multipoint Membranes.

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This folder contain cellular organelles, such as nucleus, mitochondria, ribosomes, etc.



Itemes Included in the Organelles Folder

This folder contains all necessary cellular organelles required to draw a pathway, such DNA, Nucleotides, Nucleus, Mitochondria, etc. You can view a sample of the items which are included below. To place a organelle, click on the item in the Organelle folder on the left and the organelle of choice will appear in the drawing window.



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This folder contains the membrane receptors which will be necessary to draw a signaling pathway.



Items Included in the Receptors/Channels Folder

This folder contains many types of receptors which will be required for placement on the cell membrane while drawing a signaling pathway. There many color choices for each receptor. To place a receptor, click on the receptor or choice, then a color panel will popup; in the color panel select the color type you would like, then the receptor with that color will appear in the drawing window.



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Select two items in the pathway (while holding the Ctrl key) then click on the type of signaling connector which you would like to place, the connector will automatically be placed.



The above illustrates the basic methods of drawing signaling pathways, you can view details about the other drawing items in the ePathway Illustration Items Help Files.

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This folder contain other accessory items which are required to draw some pathways, such as Phosphates, Elements (Ca, K, Na, etc.), Scissors, Syringe, Capsules, etc. You can view a sample of the Accessory Items below.



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This folder contains the basic units required to construct biochemical compounds.



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This folder contains cells and tissue types which would be found in the body.





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This folder contains organs and organ systems which would be found in the body. The organ systems are often grouped together, if you select the ungroup option in the Edit panel, you can ungroup the individual items in the organ system.







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This folder contains organisms which may be necessary to draw pathways or diagrams.





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How to Connect Items with Signaling Connectors

Step 1:
First place two items in the drawing window. While pressing the keyboard Ctrl button select one item, while still holding the Ctrl button select another item. Only two items can be selected.



Step 2:

Once the two items are selected, use the cursor to click on the type of Signal Connector (left folder) which you wish to use, such as Activation, Inhibition, Binding, etc. The signaling connector will be automatically placed. Important: the item which you select first will have the connection coming from it and pointing to the item which you select second.



Connection List:

Once items are linked with a Signaling Connector, the connection type is listed in the Connection List folder at the right side of the screen.



Step 3:

Once the Signaling Connector is placed, you can move the items and connector will move with it.



Important: If you move the arrow head or line tail away from the connected item, then when you move the item, the signaling connector will no longer move with it. The connection will still be listed in the Connection List.



Important: If you move the arrow head or line tail away from the connected item, then when you move the item, the signaling connector will no longer move with it. Inorder to re-establish the movement connection, you will need to re-position the arrow-head or tail until you see a Red Box appear around the item, then the movement connection will be established again.



Step 4:

Curving the Connector, this allows you to readjust the connection line to add curves and make the line more aesthetically pleasing. There are two bending points at the ends of the connector and one bending point in the center line of the connector which will allow you to bend the connection line.



Step 5:

Deleting the Signaling Connector, simply click on the Signaling Connector and press the Delete button on your keyboard. This will remove the Signaling Connector, as well as removing the connection of the items which was listed in the Connection List.



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