This page was last updated on June 11th, 2019 at 09:04 pm
A redocking tutorial for docking peptides with disulfide bond
In this tutorial we illustrate how to re-dock a cyclic peptide into its native receptor. We will redock a 10-mer peptide from EBV into HLA-A1101 (PDB: 5GRD).
In this tutorial you will learn:
- to generate a target file for a docking in a box defined by the known peptide.
- to run ADCP to re-dock the cyclic peptides
- to understand the output of an ADCP docking run
Prerequisites:
- You have downloaded and installed the ADFRsuite 1.0
- ADFRsuite-1.0/bin in in your path (if you use a command shell in Max OS, or Linux)
- you have downloaded and unzipped the data file associated with this tutorial.
Go back to ADCP Homepage.
Generate the target file containing the affinity maps.
First lets go to the directory for this tutorial.
For this tutorial, we will start directly from the PDBQT files. Please refer to the first tutorial on how to converting PDB files to PDBQT files.
The command produces the following output:
Perform the docking
Note we added two options compared with redocking the linear peptide.
-cys enables the potential for disulfide bond.
-nc 0.8 use native contacts as clustering criteria. We recommend using native contacts for larger peptides.
This calculation generates the following files:
- 5GRD_redocking_ranked_{num}.pdb # the final solutions with ranking after clustering
- 5GRD_redocking_{num}.pdb # the MC trajectory for each replica
- 5GRD_redocking_{num}.out # detailed output file for each replica
An example output is listed below:
Please note that docking cyclic peptide is extremely challenging, and the purpose of this tutorial is only to show the usage of ADCP. We suggest using more replicas with more Monte Carlo steps for real production runs.