BenchStab：一个用于自动化查询基于网络的稳定性预测器的工具。

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

机构信息

Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic.

Department of Information Systems, Faculty of Information Technology, Brno University of Technology, 612 00 Brno, Czech Republic.

出版信息

Bioinformatics. 2024 Sep 2;40(9). doi: 10.1093/bioinformatics/btae553.

DOI:10.1093/bioinformatics/btae553

PMID:39259175

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11427696/

Abstract

SUMMARY

Protein design requires information about how mutations affect protein stability. Many web-based predictors are available for this purpose, yet comparing them or using them en masse is difficult. Here, we present BenchStab, a console tool/Python package for easy and quick execution of 19 predictors and result collection on a list of mutants. Moreover, the tool is easily extensible with additional predictors. We created an independent dataset derived from the FireProtDB and evaluated 24 different prediction methods.

AVAILABILITY AND IMPLEMENTATION

BenchStab is an open-source Python package available at https://github.com/loschmidt/BenchStab with a detailed README and example usage at https://loschmidt.chemi.muni.cz/benchstab. The BenchStab dataset is available on Zenodo: https://zenodo.org/records/10637728.

摘要

蛋白质设计需要了解突变如何影响蛋白质稳定性的信息。为此，有许多基于网络的预测器可用，但比较它们或大量使用它们是很困难的。在这里，我们介绍了 BenchStab，这是一个控制台工具/ Python 包，可方便快捷地执行 19 个预测器，并在突变体列表上收集结果。此外，该工具可以轻松扩展其他预测器。我们创建了一个源自 FireProtDB 的独立数据集，并评估了 24 种不同的预测方法。