Requirement

The operation and display of BUMBLE have been confirmed with FireFox 3.6, Safari 4, Opera 10.10 on MacOS X Snow Leopard.
Although Google Chrome can correctly submit job and download result files, the viewer implemented with Java applet in the report page does not work.
Internet Explorer may not display the pages in an expected layout. But, it has no problem functionally.

Query submission


Job title

The job is identified by job-ID (decided by BUMBLE server), job title, and your E-mail address.
If you do not enter text here, the job will be named "untitled".

E-mail

BUMBLE server will notify this address the end of the job.

Protein

A target molecule the binding sites of which you want to predict is specified here. You can choose one of the following two way to specify it.
[!] The size of the query protein is restricted to be less than 4,000 residues and 50,000 heavy atoms.

Choose from PDB

Enter a four-letter ID of a Protein Data Bank entry and one-letter ID of a chain in the entry.

Upload your file

Upload a structure file from your computer.
BUMBLE server converts the uploaded file to .mol2 format by using OpenBabel.
The uploaded file must be written in one of file formats that can be handled by OpenBabel, and must have appropriate suffix in the file name.
[!] BUMBLE need appropriate file format, especially atom name, residue name, and order of the atoms in each residue.

Ligand

A putative ligand structure is also required.
[!] The size of the query ligand is restricted to be less than 50 heavy atoms.

Choose from PDB

Enter a three-letter ID of the ligand in the Protein Data Bank.

Upload your file

Upload a structure file from your computer.
BUMBLE server converts the uploaded file to .mol2 format by using OpenBabel.
The uploaded file must be written in one of file formats that can be handled by OpenBabel, and must have appropriate suffix in the file name.

Report


The report page is located at "http://bumble.hgc.jp/cgi-bin/report.cgi?jobid=[...]&job_title=[...]&email=[...]".
You have to remember the job ID and job title when you did not enter your email address. In this case, you can access the report page with these two parameters and "?email=unknown".
You can analyze predicted interaction hotspots and 10 predicted ligand conformations on the web by using Jmol applet.
And you can download the structure files written in PDB format by clicking button.

Query

Show the structure of query protein and ligand.

Interaction hotspots

Show coordinates of predicted interactions hotspots.

Ligand conformations

Show the predicted ligand conformations.

All

Show the all structures.
is a .tar.gz compressed file of all structures.