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A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
FACT: functional annotation transfer between proteins with similar feature architectures.
Tina Koestler1, Arndt von Haeseler, Ingo Ebersberger
1Center for Integrative Bioinformatics Vienna, Max F Perutz Laboratories, Dr Bohrgasse 9, A-1030 Vienna, Austria.
BMC Bioinformatics
|August 11, 2010
Summary
We developed the Feature Architecture Comparison Tool (FACT) to find functionally equivalent proteins, even those without sequence similarity. FACT complements existing methods, improving protein function annotation across diverse species.
Area of Science:
- Bioinformatics
- Computational Biology
- Protein Function Prediction
Background:
- Vast genomic data requires robust bioinformatics tools for protein function annotation.
- Sequence similarity is the primary method for inferring protein function but has limitations.
- Convergent evolution means functional equivalence isn't always linked to homology.
Purpose of the Study:
- Introduce the Feature Architecture Comparison Tool (FACT) for identifying functionally equivalent proteins.
- Provide a complementary approach to sequence similarity for protein function prediction.
Main Methods:
- FACT compares protein feature architectures (domains, secondary structures, composition).
- A scoring function quantifies feature architecture similarity for proteome-wide searches.
- Evaluated FACT on 9,570 EC-classified enzymes.
Main Results:
- FACT identified more functional equivalents than existing architecture-based methods.
- FACT successfully found functional equivalents with no significant sequence similarity.
- Jointly considering feature architecture and sequence similarity enhances annotation reliability.
Conclusions:
- FACT enables rapid, sensitive searches for functional protein equivalents in proteomes.
- FACT is valuable for identifying functional equivalents in distantly related species or non-homologous proteins.
- FACT enhances protein annotation, especially when combined with sequence similarity analysis.
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