ArticleJournal of molecular biology2009
OPUS-Dom: applying the folding-based method VECFOLD to determine protein domain boundaries.
Article in Journal of molecular biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Hierarchical Analysis of Protein Structures: From Secondary Structures to Protein Units and Domains.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Res-Dom: predicting protein domain boundary from sequence using deep residual network and Bi-LSTM.Bioinformatics advances · 2022Article
- Article
- Protein domain identification methods and online resources.Computational and structural biotechnology journal · 2021Review
- FUpred: detecting protein domains through deep-learning-based contact map prediction.Bioinformatics (Oxford, England) · 2020Article
- ThreaDomEx: a unified platform for predicting continuous and discontinuous protein domains by multiple-threading and segment assembly.Nucleic acids research · 2017Article
- Decomposing the space of protein quaternary structures with the interface fragment pair library.BMC bioinformatics · 2015Article
- Article
- ThreaDom: extracting protein domain boundary information from multiple threading alignments.Bioinformatics (Oxford, England) · 2013Article
- DoBo: Protein domain boundary prediction by integrating evolutionary signals and machine learning.BMC bioinformatics · 2011Article
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Authors and funding
5 authors.
Funding
Abstract
In this article, we present a de novo method for predicting protein domain boundaries, called OPUS-Dom. The core of the method is a novel coarse-grained folding method, VECFOLD, which constructs low-resolution structural models from a target sequence by folding a chain of vectors representing the predicted secondary-structure elements. OPUS-Dom generates a large ensemble of folded structure decoys by VECFOLD and labels the domain boundaries of each decoy by a domain parsing algorithm. Consensus domain boundaries are then derived from the statistical distribution of the putative boundaries and three empirical sequence-based domain profiles. OPUS-Dom generally outperformed several state-of-the-art domain prediction algorithms over various benchmark protein sets. Even though each VECFOLD-generated structure contains large errors, collectively these structures provide a more robust delineation of domain boundaries. The success of OPUS-Dom suggests that the arrangement of protein domains is more a consequence of limited coordination patterns per domain arising from tertiary packing of secondary-structure segments, rather than sequence-specific constraints.
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