PDB-score 1.0.2

A tool to massively calculate protein scores using PDB files.

PDB-score

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Features

Implements GDT scoring between a large number of predicted and actual protein models, which can be used to evaluate the prediction models.

Installation

pip install PDB-score

Usage

psc -c /path/to/control -t /path/to/treatment -o /path/to/output

• -c Directory where the experimental PDB files are stored.
• -t Directory where the predicted PDB files are stored.
• -o Directory for saving the output scores.
• -T Specify the number of cores, default is 4.
• -B Specify the Batch size, default is 5000.

Output

/path/to/output/protein_scores.csv

name	1A	2A	...	128A
Protein1	Score	Score	...	Score
Protein2	Score	Score	...	Score
...	...	...	...	...

Calculation Method

• Scores are calculated using the GDT (Global Distance Test) algorithm.
• All ligands are removed, and only the alpha carbon atoms are used to represent the residue coordinates.
• When the count of alpha carbons differs, the extra or missing residues are directly considered as failing to meet the accuracy criteria (regardless of the accuracy setting).

Performance

• Test Environment:
  • Default parameters: -T 4 -B 5000
  • Test Machine: Windows 11 PC, CPU Intel 12600k
  • Single sample size: 146KB with 154 residues
• Comparing 50,000 samples took 387061ms.
• Memory usage is less than 6GB.

Additional Notes

• Only analyzes identically named .pdb files in both input directories.
• The -o option only specifies the output directory, not the file name.
• Outputs a .csv file with a fixed file name, so be careful not to overwrite it.

Acknowledgments

• JetBrains
• ChatGPT

@SiriNatsume
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