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Updated: Mar 9, 2026
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A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
70.0K
The Use of Structural Templates in Protein Backbone Modeling
1Allelix Biopharmaceuticals 6850 Goreway Drive Mississauga, Ontario Canada , L4V 1P1.
Summary
Predicting protein structure for novel proteins with low sequence similarity is challenging. This study developed sequence profiles from structural motifs, but accuracy was low, requiring further refinement for practical use.
Area of Science:
- Structural bioinformatics
- Computational biology
- Protein structure prediction
Background:
- Protein structure modeling is established for high sequence similarity cases.
- Novel proteins with low sequence similarity (<50%) require new prediction approaches.
Purpose of the Study:
- To develop and test a novel method for predicting protein structure using sequence profiles derived from structural motifs.
- To assess the accuracy of this method for proteins with low sequence similarity.
Main Methods:
- Defined structural motif templates (icons) for helix-turn and turn-helix.
- Aligned sequences to create weighted profiles.
- Scanned the protein database for superimposable fragments to build composite templates.
- Generated sequence profiles from these templates.
- Tested profiles against the protein database for tertiary structure identification.
Main Results:
- Composite templates showed internal consistency (rmsd values ranging from 0.41 Å to 1.54 Å).
- Sequence profiles correctly identified tertiary structure in only ~10% of cases.
- Accuracy could be improved by detecting multiple occurrences of templates within a single protein.
Conclusions:
- The developed sequence profile method shows promise but requires improvement for reliable protein structure prediction.
- Detecting multiple template occurrences is a potential strategy to enhance predictive accuracy.
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