Protein Globe

The Protein Globe service has been discontinued from January 2016.

The Protein Globe is a graphical interface to the PDBj and other services.

• Summary
• What it is
• Prerequisite
• How to use
• Caveats
• • The Globe is only semi-quantitative.
  • The shapes of the continents and islands may changes their shapes, time to time.
• Making links to the Protein Globe
• • When you know all PDB ID, chain ID, and domain ID
  • When you know only PDB ID
  • Changing the colors of sea and lands

URL: https://pdbj.org//globe/globe.cgi

[Summary]

1. Each dot on the globe represents a representative of structural domains found in the Protein Data Bank.
2. Some super-clusters are represented by cartoon figures.
3. The shorter the distance between two points is, the more structurally similar are the two domains.
4. Move the sphere by dragging the mouse, and select a domain by clicking the dot.
5. Zoom out/in by shift+drag up/down.
6. Send the selected domain (dot) to other PDBj services by clicking the buttons on the top.
7. Link to a dot like, for example, https://pdbj.org//globe/globe.cgi?pdbid=1ashchain=Adomain=1
8. Don't like the colors of the sea and the lands ? Try https://pdbj.org//globe/globe.cgi?s=num where num can be a number between 0 and 59 (inclusive) or "random".

[What it is]

The Protein Globe provides a global view and representation of the protein universe. Each protein fold is represented as a point on a globe (sphere), and structurally similar folds (as judged by the ASH program) are placed closer together on the globe than structurally dissimilar folds. We can observe that there are many clusters or islands of folds on the globe. Cartoon representations of folds are provided for some large clusters.

You can interact with the Globe by using your mouse: Rotating the Globe, picking a point, etc. The Globe is an application based on jV (PDBjViewer, version 3).

[Prerequisite]

In order to use the Globe, you need to have the following softwares installed on your computer:

1. JRE (Java Run-time Environment);
2. JOGL (Java OpenGL binding).

This is because the Globe is based on jV. Please refer to the jV page for the detail.

[How to use]

1. Open the Protein Globe URL (see above).
2. Zoom, rotate, and look for some folds of interest.
3. Pick a point by clicking the point (double-clicking may be necessary with some browsers).
   • Pictures of the fold will appear on the right part of the page.
   • The picture entitledThis domainshows the structural domain of the picked point.
   • The picture entitledIn PDBshows the corresponding PDB entry as a whole.
4. By clicking the buttons just above the Globe applet, you can send this protein (chain) to other services of PDBj as a query such as PDBj Mine, Sequence Navigator, Structure Navigator, eF-site, and PDBj Mine 's jV applet.
5. Query to the SCOP and CATH structural classification databases can be also made.

[Caveats]

The Globe is only semi-quantitative.

(coming soon)

The shapes of the continents and islands may changes their shapes, time to time.

(coming soon)

[Making links to the Protein Globe]

When you know all PDB ID, chain ID, and domain ID

You can make a direct link to the protein domain on the Globe. For example, if you know that there exists on the Globe a domain with PDB ID '1ash' with chain 'A' and domain ID '1' , then you can make a link to the point by writing:

https://pdbj.org//globe/globe.cgi?pdbid=1ashchain=Adomain=1

By clicking this link, you will have the Globe with the corresponding domain focused.

When you know only PDB ID

While PDB ID and chain ID are standard PDB items, domain ID is not. Nobody can blame you if you don't know the domain ID of a particular protein fold. Thus, you can make a link to the Globe by specifying only the PDB ID like:

https://pdbj.org//globe/globe.cgi?pdbid=1ash

In this example, we are fortunate enough to have only one domain with the PDB ID '1ash' on the Globe so that the domain is automatically focused. Although the Globe page says error, this can be safely ignored in this case.

However, what if there are multiple domains with the same PDB ID on the Globe? Try the following:

https://pdbj.org//globe/globe.cgi?pdbid=2awa

This time, the Globe is not focused. But there should be three buttons on the right-center of the page, each corresponding to a domain with the PDB ID '2awa'. If you find the one you want among the buttons, click it, and you have that one focused on the Globe.

Changing the colors of sea and lands

People have likes and dislikes. Or maybe you want the Globe to be of different colors time to time for a change. By specifyingsparameter in the Globe URL, you can have the colors shown in the following figure:

You can specify the colors like:

https://pdbj.org//globe/globe.cgi?s=xy

where xy should be 0 to 59 (inclusive). the first digit (x) of xy specifies the land color, and the second digit(y) the sea. If there is no x, then only specify y (0-9). For example, by specifying 's=55', you have the dark green sea with cyan lands ( https://pdbj.org//globe/globe.cgi?s=55 ); and with 's=39', you have the grey sea and the light green lands ( https://pdbj.org//globe/globe.cgi?s=39 ), etc.

Alternatively, xy can be random (literally). In this case, the colors will be chosen randomly among the 60 choices every time the Globe is (re)loaded.