A unified approach to protein domain parsing with inter-residue distance matrix.

Kun Zhu, Hong Su, Zhenling Peng, Jianyi Yang

Bioinformatics (Oxford, England) 2023 Feb 03

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It is fundamental to cut multi-domain proteins into individual domains, for precise domain-based structural and functional studies. In the past, sequence-based and structure-based domain parsing was carried out independently with different methodologies. The recent progress in deep learning-based protein structure prediction provides the opportunity to unify sequence-based and structure-based domain parsing. Based on the inter-residue distance matrix, which can be either derived from the input structure or predicted by trRosettaX, we can decode the domain boundaries under a unified framework. We name the proposed method UniDoc. The principle of UniDoc is based on the well-accepted physical concept of maximizing intra-domain interaction while minimizing inter-domain interaction. Comprehensive tests on five benchmark datasets indicate that UniDoc outperforms other state-of-the-art methods in terms of both accuracy and speed, for both sequence-based and structure-based domain parsing. The major contribution of UniDoc is providing a unified framework for structure-based and sequence-based domain parsing. We hope that UniDoc would be a convenient tool for protein domain analysis. https://yanglab.nankai.edu.cn/UniDoc/. Supplementary data are available at Bioinformatics online. © The Author(s) 2023. Published by Oxford University Press.

Citation

Kun Zhu, Hong Su, Zhenling Peng, Jianyi Yang. A unified approach to protein domain parsing with inter-residue distance matrix. Bioinformatics (Oxford, England). 2023 Feb 03;39(2)