BenchStab is a command-line (CLI) tool for querying predictors of protein stability on the web.

This is a quick guide. For further details, please continue to the detailed documentation.

Citing

If you use our tool, please cite our paper:

Velecký, J., Berezný M., Musil M., Damborsky J., Bednar, D., Mazurenko, S., 2024: BenchStab: a tool for automated querying the web-based stability predictors. Bioinformatics 40(9)

Kindly cite also all the underlying predictors you use via this tool.

Installation

Install using pip from this repository:

pip install git+https://github.com/loschmidt/BenchStab.git

Tested environments:

• macOS 14.4.1 / pip / Python 3.9.6
• RHEL 9.4 / pip / Python 3.9.18
• Windows 11 / pip / Python 3.9.13
• Windows 10 / anaconda / Python 3.9.19

Check the installation was successful by listing all available predictors:

benchstab -l

Troubleshooting

'benchstab' is not recognized as an internal or external command, operable program or batch file.

Once the package is successfully installed, the executable is located in Python's Scripts/ directory. Please, add this directory to your PATH environment variable or use the Python installer with "Add Python to PATH" (Windows).

This problem is preceded by the following warning message from pip:
WARNING: The script benchstab.exe is installed in 'Path/To/Your/Python/Installation/Scripts' which is not on PATH.

Quick usage

• "I investigate a specific mutation, and I want to see whether the popular predictors agree on its effect on the protein stability":

echo 1CSE L45G I | benchstab

The application will acquire predictions from all implemented predictors and print the results to stdout in csv format.

• "I have a dataset prepared, and I want to query structural variants of my three favorite predictors and save the results to a file":

dataset.csv:

1CSE,L45G,I
1CSE,L45A,I
2Q98,H173A,A
1MJC,F31S,A

The command:

benchstab --include automute cupsat ddgun --pred-type structure --source dataset.csv --output path_to_results_folder/

The results will be saved to a folder named benchstab_YYMMDD_HHMMSS in a file results.csv. For more information about the output, please refer to the BenchStab output section.

Quick Python usage

• "I investigate a specific mutation, and I want to see whether the popular predictors agree on its effect on the protein stability":

from benchstab import BenchStab

client = BenchStab(input_file="input.txt")
results = client()

• "I have a dataset prepared, and I want to query structural variants of my three favorite predictors and save the results to a file":

from benchstab import BenchStab

client = BenchStab(
  input_file='dataset.csv',
  include=["automute", "cupsat", "ddgun"],
  output="path_to_results_folder/"
)
results = client()

The results will be saved in the same manner as in the CLI example.