TITLE: Ligand docking using Patchdock for Biochemistry I
AUTHORS: Chris Berndsen

[DESCRIPTION]
A protocol for JMU students to dock ligands to proteins using Patchdock

[BEFORE_START]
Have PDB file of protein and ligand

[STEPS]
SECTION: Docking setup
1. Navigate to Patchdock


SECTION: Docking setup
2. In Receptor molecule: Provide your PDB file as a RCSB code OR upload a .PDB file


 

SECTION: Docking setup
3. In Ligand molecule: Provide your PDB file as a RCSB code OR upload a .PDB file.


 

SECTION: Docking setup
6. Under Advanced Options: You can specify a binding site if you have one identified from Uniprot, COACH, BLAST or some other source.
SECTION: Docking setup
6.1. The binding site location is provided as a .txt file with the following format:


 

The number indicates the amino acid number, the letter indicates the molecule name in the receptor PDB file (usually A). 

Note: If the binding site file is not accepted, remove the letters and try again.
SECTION: Docking setup
7. Record your submission settings and add new rows as needed.


 

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4. Under Clustering RMSD: Set to 1.5 for protein-small molecule binding, 4 for protein-protein or protein-DNA docking.
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8. Press Submit Form and wait 24 to 72 hours. 
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5. Provide your email address.
SECTION: Analysis of docking
9. Open the results email to go to the table of solutions. This table contains several important pieces of information or files.

Solution No: Number of the solution
Score: Geometric shape complementarity score. The more steric clashes the lower the score. The solutions are sorted according to this score.
Area: Approximate interface area of the complex.
ACE: Atomic contact energy or the energy requried to transfer the molecule from water to protein site
PDB file of the complex: The predicted complex structure in PDB format.


 

SECTION: Analysis of docking
9.1. Record the values for the top 5 hits. Add rows as needed. You can also download the entire solutions table using a link below the table. 


 

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10. Below the table is an option to download the top X hits. Change the number to be between 5 to 10 and obtain the file.


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10.1. Name the file as


 
Replace proteinname with the receptor name, the ligandname with the ligand name.

Upload the file to OSF and provide the link to this file as note on this step.
SECTION: Visualization of docking results
11. Extract the .zip file.
SECTION: Visualization of docking results
12. Open all of the hits in a single window of a molecule visualization protein. YASARA will be used in this instance however MOL* and other software can be used.
SECTION: Visualization of docking results
12.1.   

SECTION: Visualization of docking results
13. In the example results in 12.1 most of the solutions cluster in the same area suggesting good complementarity in this region. If not specified before, the list of amino acids in this region can be used to specify a receptor site and the docking repeated to refine the placement. 
SECTION: Visualization of docking results
14. YASARA users only!

With all the solutions loaded, press the space bar to bring up the command window and type the commands shown below. The # indicates explanations that are not typed in the window.

 

Remember to replace the ligand name in the SelectRes command with the name of your ligand in YASARA.
SECTION: Visualization of docking results
14.1. An example result from the commands in Step 14.


  

SECTION: Visualization of docking results
15. Analyze the amino acids that interact with the ligands and tecord the interacting amino acids using a table with the format below. If desired add tables or rows to the table below to keep results in this protocol.



 



SECTION: Docking setup
1.1.