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Linear interacting peptides (LIPs) are intrinsically disordered regions in protein sequences that undergo disorder-to-order transition upon binding to a protein or a nucleic acid. The disordered binding regions, such as LIPs, are notoriously difficult to predict from the protein sequences, which motivated the development and release of the sequence-based CLIP predictor. Empirical evaluations show that CLIP generates relatively accurate predictions when compared to a selection of modern alternatives. We summarize the predictive architecture of CLIP, briefly discuss its predictive performance and runtime, and focus on explaining how to use its web server ( http://biomine.cs.vcu.edu/servers/CLIP/ ) and standalone package ( http://yanglab.qd.sdu.edu.cn/download/CLIP/CLIP_20220609.tar.gz ). Additionally, we demonstrate the utility of CLIP-generated results through a case study for the STAM-binding protein.

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Prediction of Disordered Linear Interacting Peptides with CLIP

  • 实验方案

  • 发表日期：

    2025年

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  • Jiahui Liang,
  • Zhenling Peng,
  • Lukasz Kurgan

摘要

Linear interacting peptides (LIPs) are intrinsically disordered regions in protein sequences that undergo disorder-to-order transition upon binding to a protein or a nucleic acid. The disordered binding regions, such as LIPs, are notoriously difficult to predict from the protein sequences, which motivated the development and release of the sequence-based CLIP predictor. Empirical evaluations show that CLIP generates relatively accurate predictions when compared to a selection of modern alternatives. We summarize the predictive architecture of CLIP, briefly discuss its predictive performance and runtime, and focus on explaining how to use its web server ( http://biomine.cs.vcu.edu/servers/CLIP/ ) and standalone package ( http://yanglab.qd.sdu.edu.cn/download/CLIP/CLIP_20220609.tar.gz ). Additionally, we demonstrate the utility of CLIP-generated results through a case study for the STAM-binding protein.