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A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Feature amplified voting algorithm for functional analysis of protein superfamily
Che-Lun Hung1, Chihan Lee, Chun-Yuan Lin
1Department of Computer Science, National Tsing Hua University, 101, Section 2 Kuang Fu Road, Hsinchu, Taiwan.
BMC Genomics
|December 15, 2010
Summary
The Feature Amplified Voting Algorithm with Three-profile alignment (FAVAT) method effectively identifies functionally important amino acids in protein superfamilies. This approach aids in understanding protein function, especially when sequence data is limited.
Area of Science:
- Biochemistry
- Structural Biology
- Bioinformatics
Background:
- Identifying functional regions in proteins is crucial in the post-genomic era.
- Traditional methods struggle with divergent protein superfamilies where function doesn't align with phylogeny.
- Amino acid sequence analysis is vital when structural information is unavailable.
Purpose of the Study:
- To introduce the Feature Amplified Voting Algorithm with Three-profile alignment (FAVAT) for identifying functional residues.
- To demonstrate FAVAT's capability in detecting critical amino acids in divergent protein families.
- To validate FAVAT using the amidohydrolase superfamily.
Main Methods:
- Developed the Feature Amplified Voting Algorithm with Three-profile alignment (FAVAT).
- Applied FAVAT to identify critical residues in mammalian imidase within the amidohydrolase superfamily.
- Classified superfamily members by functional properties and organism sources.
- Compared FAVAT results with existing methods like Multiple Sequence Alignment (MSA).
Main Results:
- FAVAT successfully identified key residues in mammalian imidase, including those involved in metal ion coordination.
- The algorithm corrected misidentification of residues by MSA, such as Asp57.
- Several functionally and structurally relevant amino acid residues were accurately predicted.
Conclusions:
- FAVAT is effective in predicting functionally important amino acids within the amidohydrolase superfamily.
- The strategy leverages discrepancies between sequence and function to identify key residues.
- FAVAT shows potential applicability to other protein families for functional residue prediction.
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