Download
Click here to download the MDockPeP2_VS program (version 1.0).
Click here to download data presented in the manuscript.
Reference:
- Xu X, Kao W-L, Wang A, Lee H-J, Duan R, Holmes H, Gallazzi F, Ji J, Sun H, Heng X, Zou X. In silico screening of protein-binding peptides with an application to developing peptide inhibitors against antibiotic resistance. PNAS Nexus 2024, pgae541. DOI: https://doi.org/10.1093/pnasnexus/pgae541
Installation instructions
MDockPeP2_VS is a structure-based in silico peptide screening program. It is written in python2.7 and utilizes several third-party programs, including a modified version of AutoDock Vina (vina_pep), PCalign , and Naccess. MDockPeP2_VS has been tested on Linux systems.
To install MDockPeP2_VS, uncompress the file mdockpep2_vs.tar.gz with:
tar -zvxf mdockpep2_vs.tar.gz
This will create a directory "mdockpep2_vs" containing the following subdirectories:
-- pep_lib: contains a peptide library constructed by fragments in monomeric protiens from Protein Data Bank. Uncompress the file helical_pep_10_15.tar.gz with:
tar -zvxf helical_pep_10_15.tar.gz
-- programs: contains the program vina_pep, a modified version of AutoDock vina.
-- examples: contain a test case for running MDockPeP2_VS.
In the main mdockpep2_vs directory, you will find the main program of MDockPeP2_VS named as 'mdockpep2_vs.py', which is written in python 2.7.
To run mdockpep2_vs.py, use the following command to set executable permission for the script:
chmod +x mdockpep2_vs.py
Usage: ./mdockpep2_vs.py --config arg
./mdockpep2_vs.py -h
The following is an example of the configure file:
# The target protein in PDBQT format
receptor = rec.pdbqt
# The center of the docking box
center_x = 36.9
center_y = 25.0
center_z = 48.1
# size of the box in Angstrom
size_x = 36
size_y = 30
size_z = 20
# independent runs in vina_pep, default = 64
exhaustiveness = 64
# number of cpu used for the program
cpu = 6
# The range of peptide sequence length for screening
pep_len_min = 10
pep_len_max = 15
# The number of output peptides, default = 1000
out_num = 1000
Before running mdockpep2_vs.py, ensure that the third-party program PCalign is installed, and its location ("pcprepare_bin" and "pcalign_bin") are correctly set in 'mdockpep2_vs.py'. Also, ensure that the paths for mdockpep2_vs ("mdockpep2vs_path") and peptide library ("pep_path") are properly configured in "mdockpep2_vs.py".
IMPORTANT: We strongly recommend running the test case in the example folder using the option "--test on" before conducting a large-scale screening study.
cd examples/test/
../../mdockpep2_vs.py --config conf.txt --test on
In the main directory, you will find a program named "final_filter.py", which can be used to apply various filters to the outputs of mdockpep2_vs.py.
"final_filter.py" utilizes the third-party program Naccess (http://www.bioinf.manchester.ac.uk/naccess/).
Usage: ./final_filter.py rec.pdb mdockpep2vs_out_models.pdb mdockpep2vs_out_sequences.txt