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Updated: May 10, 2026
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A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
ThreaDom: extracting protein domain boundary information from multiple threading alignments
Zhidong Xue1, Dong Xu, Yan Wang
1Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
Bioinformatics (Oxford, England)
|July 2, 2013
Summary
A new computational method, ThreaDom, accurately predicts protein domain boundaries using multiple threading alignments. This approach improves the identification of both single and discontinuous domains, crucial for protein function annotation.
Area of Science:
- * Structural bioinformatics
- * Computational biology
- * Protein domain analysis
Background:
- * Protein domains are independently folding and evolving units, essential for protein function annotation.
- * Current sequence-based methods lack accuracy, especially for discontinuous domains.
- * Template-based methods are efficient for 3D structure modeling, suggesting combined alignment information can improve domain prediction.
Purpose of the Study:
- * To develop an efficient computational method for predicting protein domain boundary locations.
- * To improve the accuracy and reliability of domain prediction, particularly for discontinuous domains.
- * To leverage multiple threading alignment information for enhanced domain identification.
Main Methods:
- * Developed ThreaDom, a novel protein domain predictor utilizing multiple threading alignments.
- * Derived a domain conservation score integrating template domain structures and alignment gaps.
- * Evaluated performance on non-redundant sequences and proteins with discontinuous domains.
Main Results:
- * ThreaDom achieved 81% accuracy in single- and multi-domain classification on 630 sequences.
- * 78% of domain linkers were assigned within ±20 residues.
- * On discontinuous domains, ThreaDom showed 84% precision and 65% recall.
- * Performance on CASP8, CASP9, and CASP10 targets significantly outperformed other domain predictors.
Conclusions:
- * ThreaDom offers a significant advancement in computational protein domain prediction.
- * The method effectively identifies both single and discontinuous protein domains.
- * ThreaDom's accuracy and reliability are demonstrated through rigorous testing on benchmark datasets and CASP targets.
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