Structure Alignment Using Geometric Measures
Author Information
Author(s): Peter L Chang, Andrew W Rinne, T Gregory Dewey
Primary Institution: Keck Graduate Institute of Applied Life Sciences
Hypothesis
Can the writhing number be used as a local geometric measure for protein structure alignment?
Conclusion
The study demonstrates that using the writhing number as a geometric measure allows for high-quality structure alignments using standard sequence alignment algorithms.
Supporting Evidence
- The writhing number provides a local geometric profile of proteins.
- The method allows for fast database searching and multiple structure alignment.
- TLOCAL outperformed existing methods for difficult protein alignments.
Takeaway
This study shows a new way to compare protein shapes by looking at how they twist and bend, which helps scientists understand their functions better.
Methodology
The study used a sliding window approach to calculate the writhing number along protein chains and encoded these into a geometric alphabet for alignment.
Limitations
The method does not provide a direct three-dimensional representation of the alignments.
Digital Object Identifier (DOI)
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