pyCAST, a Python package for the detection of cavities on surface proteins.

IF 4.1 2区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Computational and structural biotechnology journal Pub Date : 2025-08-11 eCollection Date: 2025-01-01 DOI:10.1016/j.csbj.2025.07.054

Giorgio Luciano, Ulderico Fugacci, Silvia Biasotti

引用次数: 0

Abstract

Identifying enzymatic activity sites, signal transduction pathways, and binding sites is crucial in biochemical research, prompting various methodologies. This study introduces pyCAST, a Python package designed to detect cavities on protein surfaces using the CAST methodology, a widely recognized approach for cavity identification. The paper describes the principle of the CAST methods and presents our implementation, including the results achieved over benchmark data sets. Furthermore, it discusses the limitations of the technique and potential future improvements. pyCAST is user-friendly, modular, adaptable to diverse applications, and openly available under the MIT license.

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pyCAST，一个Python包，用于检测表面蛋白质上的空腔。

确定酶活性位点、信号转导途径和结合位点在生化研究中至关重要，促使了各种方法的产生。本研究介绍了pyCAST，一个Python包，旨在使用CAST方法检测蛋白质表面的空腔，这是一种广泛认可的空腔识别方法。本文描述了CAST方法的原理，并介绍了我们的实现，包括在基准数据集上取得的结果。此外，它还讨论了该技术的局限性和潜在的未来改进。pyCAST是用户友好的、模块化的、适用于各种应用程序的，并且在MIT许可下公开可用。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Computational and structural biotechnology journal Biochemistry, Genetics and Molecular Biology-Biophysics

CiteScore

9.30

自引率

3.30%

发文量

540

审稿时长

6 weeks

期刊介绍： Computational and Structural Biotechnology Journal (CSBJ) is an online gold open access journal publishing research articles and reviews after full peer review. All articles are published, without barriers to access, immediately upon acceptance. The journal places a strong emphasis on functional and mechanistic understanding of how molecular components in a biological process work together through the application of computational methods. Structural data may provide such insights, but they are not a pre-requisite for publication in the journal. Specific areas of interest include, but are not limited to: Structure and function of proteins, nucleic acids and other macromolecules Structure and function of multi-component complexes Protein folding, processing and degradation Enzymology Computational and structural studies of plant systems Microbial Informatics Genomics Proteomics Metabolomics Algorithms and Hypothesis in Bioinformatics Mathematical and Theoretical Biology Computational Chemistry and Drug Discovery Microscopy and Molecular Imaging Nanotechnology Systems and Synthetic Biology