DoBi

Introduction

DoBi is a tool for predicting the binding sites on pair of given proteins. DoBi is implemented in Java. To run DoBi, Sun's Java Running Environment (JRE) 6.0 is required. If JRE is not installed, please go to http://java.sun.com/ to download and install the JRE.
 

Download program

  1. Click here to download the executable program DoBi.jar.
  2. Click here to download sites.pdb, which stores the binding sites predicted by DoBi for 1qa9(A:B).
  3. Click here to download structure.pdb, which stores the conformation discovered by DoBi for 1qa9(A:B).
  4.    
PS: The program will work few minutes. The PDB file (http://www.rcsb.org/pdb) of the proteins are needed for prediction, so the computer running program must connect to the Internet.
 

Run DoBi

To run the DoBi program, you need to type a command line. Four arguments are required.  
(1) the PDB code
of a protein chain;
(2) the PDB code of another protein chain;
(3) output file path of the prediction binding sites;
(4) output file path of the prediction structure;
Example for operation: Suppose the calculated proteins are "1qa9A" and "1qa9B", and you want to save the output sites as "D:\sites.pdb" and structure as "D:\structure.pdb". You should use the command:
DoBi.jar  1qa9A  1qa9B  D:\sites.pdb  D:\structure.pdb  
PS: The PDB code of a similar protein chain consists of five letters. The first four letter code indicates the PDB ID, and the fifth letter means the chain ID. For example, "1qa9A" is the chain A of the protein 1qa9. If a protein has only one chain, the fifth letter can be replaced by underline, such as "1hnf_".
 

Output File 

The output file contains a list of the binding sites. The following is the report for the prediction interface:
 

 

 

Graphical view

The output file can be used as input file for PyMOL to show 3D structure. The pairs of sites for 1qa9A and 1qa9B are as follow:

 

 

PyMOL is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry. For more documentation and updated information, check the PyMOL website.

 

System Environment

We have implemented the algorithms in Java. The software package can run on Windows, and the computer running program must connect to the Internet. We suggest that you must use the IE browser to access this websit.

Author

Fei Guo, Shuai Cheng Li, Lusheng Wang
 
ċ
DoBi.jar
(40k)
C S,
Oct 25, 2011, 10:03 PM
ċ
sites.pdb
(2k)
C S,
Sep 25, 2011, 12:32 AM
ċ
structure.pdb
(130k)
C S,
Sep 25, 2011, 12:32 AM
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