BenchStab: a tool for automated querying of web-based stability predictors.

Area of Science:

• Computational biology
• Protein engineering
• Bioinformatics

Background:

• Accurate prediction of protein stability changes upon mutation is crucial for protein design.
• Numerous web-based tools exist for predicting protein stability, but their disparate nature hinders comparative analysis and large-scale application.
• A unified platform is needed to streamline the execution and comparison of multiple protein stability prediction methods.

Purpose of the Study:

• To develop BenchStab, a versatile console tool and Python package for executing multiple protein stability predictors.
• To facilitate the comparison and analysis of protein mutation effects on stability.
• To provide an extensible framework for integrating new prediction tools.

Main Methods:

• BenchStab was developed as an open-source Python package.
• It supports the execution of 19 different protein stability prediction tools.
• An independent dataset was created from FireProtDB for evaluation purposes.

Main Results:

• BenchStab enables the rapid execution and collection of results from numerous protein stability predictors.
• The tool's design allows for easy extension with additional prediction methods.
• An evaluation was performed on 24 distinct prediction methods using a curated dataset.

Conclusions:

• BenchStab simplifies the process of assessing how mutations impact protein stability.
• The tool enhances the efficiency of comparative analysis of protein stability predictors.
• BenchStab is a valuable resource for protein design and engineering research.