This page explains an example of predictions by BUMBLE.
Here, G-alpha-13 / GDP complex (PDB: 1zcb) was used as the example.
At begin with, open the main page of the server.
Query protein and ligand will be submitted from this page.
As a first step, you would enter "Job title" and "E-mail".
They are options. When you enter your e-mail address, the server will inform you the end of your job with e-mail.
Next, the query protein and ligand should be specified. You can choose one of the two ways.
- Select a structure from the Protein Data Bank.
- Upload a structure file from your PC.
In the latter way, the server accepts files written in .pdb, and .mol2 fromats.
Here, we select the former way and fill out the forms as follows:
- Protein PDB-ID: 1zcb
- Protein Chain-ID: A
- Ligand 3-letter ID: GDP
And then, push the "submit" button.
When the job is successfully submitterd, following message will be displayed.
The URL indicates a report page of the job.
If you entered your E-mail address, you will receive the mail from the server, when the job is finished.
After a calculation, you can download structure files of predicted conformations from the report page.
Moreover, you can also briefly analyse the result via GUI of Jmol applet in the report page.
The basic information of the job is displayed at next to the header.
The left part is a viewer for molecule geometries.
You can manupilate the view as follows:
- left-drag: rotate
- wheel or shift+left-drag: zoom
The structure files of molecules (written in .pdb format) can be downloaded from button.
Here, enable the checkbox for "Hotspot".
The spheres were widely distributed, but there was a large cluster around the first-ranked conformation.
Next, show the all of predicted conformations.
There were three groups of the predicted conformations.
The group consisted of rank 1, 3, 4, 8, 9, 10 and anoter one consisted of rank 2, 5, 6 shared binding site of the phosphate group. Rank 7 was located at far from others.
This figure shows superimposing of the native and rank 1 conformations.
Although the predicted conformation was slightly distorted, the binding site and orientation was correctly predicted.
[!] This program contains stochastic process. You may obtain a result that is differ from this example, when the same query is submitted.