AlphaFoldDB_Processing

This script can clean up the disordered region in the AlphaFold DB structures to adapt it to the molecular docking, extract the sequence of the disordered region to make it available for sequence motif searching.

Introduction

Traditional methods explore potential Protein-Protein Inteaction and Protein-Ligand Interaction by molecular docking. The molecular docking is highly dependent on the protein structure, the Alphafold DB gives us a large amount of high quality structures. Howerver, many low confidence structures of disordered regions let it difficult for these structures to be used for molecular docking.

Here, we provide a scirpt (Domain_Parser.jl) to extract ordered structures from the structure of alphafold DB for molecular docking.

Many disordered regions play critical roles in protein-protein interactions, and we also provide an additional script (Disorder_Reader.jl) to extract the sequences of disordered regions from alphafold DB for motif searching.

Dependencies

1. Julia
2. BioStructures library in julia.

Installtion

1. Install Julia on your computer, Linux, macOS or Windows.
2. run Julia, click julia.exe on windows, run julia on Linux or macOS.
3. typing ]add BioStructures in RPEL and pressing enter to add BioStructures library in julia.

Usage

Linux:

To read the disorder region from AF2 structures.

julia -p 8 Disorder_Reader.jl

To extract the ordered regions from AF2 structures.

julia -p 8 Domain_Parser.jl

Windows:

Drag scripts to your working directory containing your AF2 DB folder， then clicking scripts and select julia.exe to run:

Typing your AF2_DB foldername in the cmd and running it.

Try to modify the scripts

There are a series of global variables that can be modified in the script.

global b_factor_max = 100 # max b_factor(pLDDT) to keep a residue.
global b_factor_min = 50 # min b_factor(pLDDT) to keep a residue.
global disorder_len_max = 5 # the max disorder tail in a ordered domain.
global domain_min_len = 10   # this option is means of the min length of fargs. The domain is consist of frags incessant in sequence.
global min_dist_interdomain = 3.50  # 3.00 is a very strict cutoff.
global min_Adjacent_residues = 5 # How many residues are close together between frags will be identified as a domain.

Citation

@article{doi:10.1021/acs.jcim.2c01033,
author = {Wang, Lin and Li, Feng-lei and Ma, Xin-yue and Cang, Yong and Bai, Fang},
title = {PPI-Miner: A Structure and Sequence Motif Co-Driven Protein–Protein Interaction Mining and Modeling Computational Method},
journal = {Journal of Chemical Information and Modeling},
volume = {62},
number = {23},
pages = {6160-6171},
year = {2022}
}