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A unified approach to protein domain parsing with inter-residue distance matrix.
- Source :
-
Bioinformatics . Feb2023, Vol. 39 Issue 2, p1-7. 7p. - Publication Year :
- 2023
-
Abstract
- Motivation 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. Results 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. Availability and implementation https://yanglab.nankai.edu.cn/UniDoc/. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]
Details
- Language :
- English
- ISSN :
- 13674803
- Volume :
- 39
- Issue :
- 2
- Database :
- Academic Search Index
- Journal :
- Bioinformatics
- Publication Type :
- Academic Journal
- Accession number :
- 164277601
- Full Text :
- https://doi.org/10.1093/bioinformatics/btad070