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Comparison of sequence and structure alignments for protein domains
Aron Marchler-Bauer1, Anna R Panchenko, Naomi Ariel
1Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894, USA.
Proteins
|July 12, 2002
Summary
Protein domain alignments from sequence and structure comparisons largely agree. However, structure-based alignments better identify homologous regions and improve molecular model accuracy, especially for low sequence similarity.
Area of Science:
- Computational Biology
- Bioinformatics
- Structural Biology
Background:
- Profile search methods rely on protein domain alignments for comparative sequence analysis.
- Existing methods primarily use sequence comparison for domain alignment.
- The increasing protein structure database enables structure comparison for domain alignment.
Purpose of the Study:
- To assess the agreement between protein domain alignments derived from sequence and structure comparisons.
- To evaluate the consistency in identifying homologous regions and residue sites.
- To determine the impact on molecular model accuracy.
Main Methods:
- Comparison of domain alignments computed by sequence and structure comparison methods.
- Assessment of homologous region identification (domain boundary location).
- Evaluation of homologous residue site identification and predicted molecular model accuracy.
Main Results:
- Domain alignments from sequence and structure comparisons show substantial consistency.
- Sequence-based alignments often identify shorter homologous regions than structure-based ones.
- Sequence-based alignments yield less accurate molecular models at low sequence similarity.
Conclusions:
- Structure comparison provides more accurate identification of homologous regions and residue sites.
- Integrating structure comparison data can enhance domain alignment collections.
- Improved domain alignments can boost the performance of profile search methods.