PUNCH：用于预测蛋白质序列内在无序区域的交互式Web服务器。

IF 4.7 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Biology Pub Date : 2025-02-21 DOI:10.1016/j.jmb.2025.169018

Di Meng, Gianluca Pollastri

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引用次数: 0

摘要

PUNCH是一个免费访问的web服务器，旨在快速准确地预测蛋白质序列中的内在无序区（idr）。建立在高性能计算框架上，PUNCH web服务器建立在PUNCH2-Light predictor上，结合了速度和预测精度，为用户提供了一个简化的界面，用于从序列输入生成预测。通过对CAID2基准数据集的验证，PUNCH web服务器在检测不同蛋白质序列的idr方面表现出具有竞争力的性能。值得注意的是，它在Disorder_PDB数据集上表现出色，并为Disorder_NOX数据集提供了可靠的结果，解决了预测序列相似度低的无序区域的挑战。该服务器可在https://alienlabs.ucd.ie/punch2/上获得，具有广泛的文档和可下载的示例数据集，以支持结构生物学和生物信息学的研究人员。

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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PUNCH: An Interactive Web Server for Predicting Intrinsically Disordered Regions in Protein Sequences.

PUNCH is a freely accessible web server designed for the rapid and accurate prediction of intrinsically disordered regions (IDRs) in protein sequences. Built on a high-performance computational framework, PUNCH web server which built on PUNCH2-Light predictor, combines speed with predictive accuracy, offering users a streamlined interface for generating predictions from sequence input. Validated against the CAID2 benchmarking datasets, PUNCH web server demonstrates competitive performance in detecting IDRs across diverse protein sequences. Notably, it excels in the Disorder_PDB dataset and provides reliable results for the Disorder_NOX dataset, addressing the challenges of predicting disordered regions with low sequence similarity. The server is available at https://alienlabs.ucd.ie/punch2/, with extensive documentation and downloadable example datasets to support researchers in structural biology and bioinformatics.

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来源期刊

Journal of Molecular Biology 生物-生化与分子生物学

CiteScore

11.30

自引率

1.80%

发文量

412

审稿时长

28 days

期刊介绍： Journal of Molecular Biology (JMB) provides high quality, comprehensive and broad coverage in all areas of molecular biology. The journal publishes original scientific research papers that provide mechanistic and functional insights and report a significant advance to the field. The journal encourages the submission of multidisciplinary studies that use complementary experimental and computational approaches to address challenging biological questions. Research areas include but are not limited to: Biomolecular interactions, signaling networks, systems biology; Cell cycle, cell growth, cell differentiation; Cell death, autophagy; Cell signaling and regulation; Chemical biology; Computational biology, in combination with experimental studies; DNA replication, repair, and recombination; Development, regenerative biology, mechanistic and functional studies of stem cells; Epigenetics, chromatin structure and function; Gene expression; Membrane processes, cell surface proteins and cell-cell interactions; Methodological advances, both experimental and theoretical, including databases; Microbiology, virology, and interactions with the host or environment; Microbiota mechanistic and functional studies; Nuclear organization; Post-translational modifications, proteomics; Processing and function of biologically important macromolecules and complexes; Molecular basis of disease; RNA processing, structure and functions of non-coding RNAs, transcription; Sorting, spatiotemporal organization, trafficking; Structural biology; Synthetic biology; Translation, protein folding, chaperones, protein degradation and quality control.