uid2TM

This Python script automates the process of comparing protein structures by downloading their PDB files from the AlphaFold protein structure database, computing their radius of gyration (Rg), aligning the structures using TM-align, and extracting key metrics like RMSD, TM-score, and aligned length. The results are saved in a CSV file for each protein pair provided in the input CSV. Based on statistics:

• 0.0 < TM-score < 0.30, random structural similarity
• 0.5 < TM-score < 1.00, in about the same fold

How to run the script:

This repository contains two main scripts:

• uid2TM_conda.py
• uid2TM.py The choice of script depends on which version of TM-align you are using. Both scripts calculate:
• Radius of gyration of the protein
• Root Mean Square Deviation
• TM-scores

However, the "uid2TM_conda.py" script, designed for use in a Conda environment, additionally generates input files for visualizing aligned protein chains in PyMOL. The "uid2TM.py" script, in contrast, provides only the calculated values without generating PyMOL input, making it more computationally and storage-efficient for large-scale analyses.

Input:

A CSV file containing columns: prefix, uid1, and uid2.

• prefix: An index for each protein pair.
• uid1 and uid2: UniProt IDs of the two proteins to be aligned. A working directory path to save the downloaded PDB files and results.

Output:

A CSV file named <youinputname_TMscore.csv> containing the following columns inaddition to the columns in the input file:

• Rg1: Radius of gyration of protein 1.
• Rg2: Radius of gyration of protein 2.
• RMSD: Root Mean Square Deviation from the TM-align output.
• TM-Score: TM-align score for protein alignment.
• Aligned Length: Number of aligned residues between the two proteins.

Requirements:

TM-align Installation

For the uid2TM.py script

Download and compile TM-align from the Zhang Lab site. Click here.

g++ -static -O3 -ffast-math -lm -o TMalign TMalign.cpp

Ensure TM-align is in your PATH by adding the following to ~/.bashrc, replacing /path/to/TMalign with the actual path:

export TMalign="/path/to/TMalign"

Save and exit the editor, then reload the shell configuration:

source ~/.bashrc

Confirm the installation:

TMalign -h

For uid2TM_conda.py script

Install TM-align via Conda following these instructions :

conda install -c schrodinger pymol conda install -c schrodinger pymol-psico conda install -c speleo3 tmalign

After installation, add the path to TM-align to your PATH. Replace /path/to/tmalign with the actual directory containing the TM-align executable:

export PATH="$PATH:/path/to/tmalign"

Save and exit the editor, then reload the shell configuration:

source ~/.bashrc

Confirm the installation:

TMalign -h

Additional Python Packages

Install these packages (BioPython, Pandas, Requests, Numpy) with pip3:

pip3 install biopython pandas requests numpy

MDAnalysis

pip3 install MDAnalysis --only-binary :all: