PDBCor

Extraction of correlations from multistate PDB protein coordinates

Installation

Required software:

• Python 3

1. Download the latest PDBcor wheel (pdbcor-x.y.z-py3-none-any.whl)

2. Set up a new python environment & install PDBcor:

python3 -m venv venv
source venv/bin/activate
pip install pdbcor-x.y.z-py3-none-any.whl

Shell script

Analyse correlations of your multistate protein bundle directly via the shell entry-point to PDBcor:

# Demo example
pdbcor demo.pdb

Parameters:
	bundle: str, path to the pdb file
	--nstates: int, number of protein states, deafult=2
	--mode: str, mode of correlations, deafult=backbone can be one of the following: backbone - calculate correlations in protein backbone sidechain - calculates correlations in protein sidechain combined - calculates overall correlations full - subsequently calculated backbone, sidechain and combined correlations
	--therm_fluct: float, amplitude of the thermal motion, default=0.5
	--therm_iter: int, number of thermal simulations, default=1
	--loop_start: int, start of the loop (residue index), default=-1
	--loop_end: int, end of the loop (residue index), default=-1

Python package

Implement your own code in Python:

from pdbcor import CorrelationExtraction

# Prepare correlation extractor (demo example)
a = CorrelationExtraction(
    "demo.pdb",
    mode="backbone",
    nstates=2,
)

# Run calculation
a.calculate_correlation()

Produced output

Whether running from the shell or via Python, outputs are combined in the folder /correlations, which is created in the parent directory of the source PDB file.

Outputs include distance and angular correlation results including:

• text file with correlation parameters of your bundle and state populations (correlations_{mode}.txt)
• lists of correlations between each pair of residues ({ang,dist,cross}_ig_{mode}.csv)
• correlation heatmaps (heatmap_{ang,dist,cross}_{mode}.png)
• histograms of correlation parameters (hist_{ang,dist}_{mode}.png)
• sequential correlation parameter charts per residue (seq_{ang,dist}_{mode}.png)
• chimera executable to visualize a multistate bundle (bundle_vis_{mode}.py)