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ADVICE: Automated Detection and Validation of Interaction by Co-Evolution.
Soon-Heng Tan1, Zhuo Zhang, See-Kiong Ng
1Knowledge Discovery Department, Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613, Singapore. soonheng@i2r.a-star.edu.sg
Nucleic Acids Research
|June 25, 2004
Summary
The Automated Detection and Validation of Interaction by Co-Evolution (ADVICE) tool predicts protein-protein interactions by analyzing co-evolution patterns. It helps validate experimental data and identify spurious interactions based on evolutionary history similarities.
Area of Science:
- Bioinformatics
- Computational Biology
- Evolutionary Biology
Background:
- Protein-protein interactions (PPIs) are crucial for cellular functions.
- Co-evolutionary analysis leverages shared evolutionary histories of interacting proteins.
- Existing methods for PPI prediction can be computationally intensive or lack validation.
Purpose of the Study:
- To develop and present the ADVICE web tool for predicting and validating protein-protein interactions.
- To automate the quantification of evolutionary history similarities between proteins.
- To provide a resource for validating experimental PPI data and identifying false positives.
Main Methods:
- Utilizes the principle that interacting proteins exhibit coordinated evolutionary changes.
- Accepts protein sequences or pairs as input.
- Retrieves orthologous sequences to compute evolutionary history similarities.
- Visualizes co-evolved proteins as networks to aid hypothesis generation.
Main Results:
- ADVICE successfully automates the co-evolutionary analysis for PPI prediction.
- The tool can distinguish between likely and unlikely interacting protein pairs based on evolutionary signals.
- Provides a network visualization feature for exploring predicted interactions.
Conclusions:
- ADVICE offers an automated and efficient approach for predicting and validating protein-protein interactions.
- The tool serves as a valuable resource for researchers in molecular biology and bioinformatics.
- It enhances the reliability of PPI data by integrating evolutionary evidence.
