ATPdock:

A template-based method for ATP-specific protein-ligand docking.

Pre-requisite:

- Python3, Java
- MGLTools software (http://mgltools.scripps.edu/downloads)
- OpenBabel software (http://openbabel.org/wiki/Category:Installation)
- Linux system

Installation:

*Install and configure the softwares of Python3, Java, MGLTools and OpenBabel in your Linux system. Please make sure that python3 includes the modules of 'os', 'math', 'numpy', 'random', 'subprocess', 'sys', and 'shutil'. If any one modules does not exist, please using 'pip3 install XXXX' command install the python revelant module. Here, "XXXX" is one module name.

*Download this repository at https://github.com/jun-csbio/ATPdock.git. Then, uncompress it and run the following command lines on Linux System.

  $ chmod -R 777 ./software
  $ chmod -R 777 ./basefile
  $ java -jar FileUnion.jar ./PLDB/ ./PLDB.tar.gz
  $ rm -rf ./PLDB
  $ tar zxvf PLDB.tar.gz
  $ cp [THE INSTALLATION PATH OF MGLTools]/bin/pythonsh ./basefile
  $ cp [THE INSTALLATION PATH OF MGLTools]/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py ./basefile
  $ cp [THE INSTALLATION PATH OF MGLTools]/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_receptor4.py ./basefile

NOTE THAT, [THE INSTALLATION PATH OF MGLTools] SHOULD BE THE MGLTools INSTALLATION PATH.

*The file of "Config.properties" should be set as follows:

PPSALIGN_EXE_ABSOLUTE_PATH=[THE ABSOLUTE PATH OF ATPDOCK]/software/PPSalign
APOC_EXE_ABSOLUTE_PATH=[THE ABSOLUTE PATH OF ATPDOCK]/software/apoc
PPSSEARCH_DATABASE_ABSOLUTE_PATH=[THE ABSOLUTE PATH OF ATPDOCK]/PLDB

NOTE THAT, THE ABOVE [THE ABSOLUTE PATH OF ATPDOCK] SHOULD BE THE ABSOLUTE PATH OF THE DOWNLOADED AND xx ATPDOCK PACKAGE, e.g., /home/junh/ATPdock-main

Prepare the query folder (see the "example" folder)

*The query folder have to only contain three files, i.e., "pdb.pdb", "tem.txt", "pdb.site". Please make sure that the query folder only contains the above three files.

"pdb.pdb" contains the 3D structure information of the query receptor protein in PDB format.

"tem.txt" has two lines: 1) the first line is sequence identity cutoff, ranging from 0.3 to 1 (suggested 0.3); 
                         2) the second line is searched ligand type. If only search for template proteins that bind to ATP and ADP, the second line is ~ATP~~ADP~. If all ligand types are allowed, the second line is NULL. More ligand type information could be found at https://zhanglab.ccmb.med.umich.edu/BioLiP/ligand.html. For example,
        0.3
        ~ATP~~ADP~~AMP~~GTP~~GDP~

"pdb.site" is the information of binding residue type and index. In this file, each line means one pocket. User can define multiple binding pockets of the protein. For example, if one protein has two binding pockets, there are two lines, i.e.,
        V10 G38 C39 G40 R61 P89 G90 D91 G92 K93
        E65 I66 V67 N104 R106

NOTE THAT, IF YOU DONOT KWON THE ATP-BINDING POCKET INFORMATION OF THE QUERY PROTEIN, WE STRONGLY SUGGESTED THAT USING THE WEB-SERVER OF ATPbind (https://zhanglab.ccmb.med.umich.edu/ATPbind/) TO PREDICTED ITS BINDING POCKETS. BASED ON THE ATPbind-PREDICTED POCKET, PREPARING THE FILE OF "pdb.site".

Run

  $ python3 ATPdock.py [ABSOLUTE PATH OF THE QUERY FOLDER]

NOTE THAT, [ABSOLUTE PATH OF THE QUERY FOLDER] SHOULD BE THE ABSOLUTE PATH OF THE QUERY FOLDER, e.g., /home/junh/ATPdock-main/example.

The docking result

*The docking result of each pocket should be found in the outputted folder, i.e., "ATPx", where "x" is the pocket index number. In each "ATPx" folder, the ATP docking pose could be found in the file of "final.pdb".

Update History:

• First release 2021-05-31 (see https://github.com/brightrao/ATPdock/)
• Update PPS-search 2021-07-28

References

[1] Liang Rao, Ning-Xin Jia, Jun Hu, Dong-Jun Yu, and Gui-Jun Zhang. ATPdock: a template-based method for ATP-specific protein-ligand docking. Bioinformatics. sumitted.