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A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
A protein block based fold recognition method for the annotation of twilight zone sequences
V Suresh1, K Ganesan, S Parthasarathy
1Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India.
Protein and Peptide Letters
|May 18, 2012
Summary
Protein Blocks, a set of 16 structural fragments, improve protein backbone description. This method uses Protein Blocks for fold recognition in twilight zone sequences, achieving 35.5% accuracy.
Area of Science:
- Structural biology
- Bioinformatics
Background:
- Traditional secondary structure descriptions (Helix, Sheet, Coil) are limited.
- Structural Alphabets, like Protein Blocks, offer a more detailed protein backbone description.
- Protein Blocks consist of 16 unique 5-residue fragments.
Purpose of the Study:
- To develop a protein fold recognition method using Protein Blocks.
- To annotate twilight zone sequences, which are difficult to classify.
- To assess the effectiveness of Protein Blocks in fold recognition.
Main Methods:
- Utilizing Protein Blocks (16 structural fragments) for sequence analysis.
- Aligning predicted Protein Blocks of query sequences with a library of 953 known folds.
- Employing local pair-wise alignment with specific z-value (≥ 2.5) and P-value (≤ 0.08) thresholds for prediction.
Main Results:
- The method successfully recognized possible folds for 35.5% of twilight zone sequences.
- The accuracy is based on predicted Protein Block sequences generated by pb_prediction.
- The Protein Blocks library encompasses 953 known protein folds.
Conclusions:
- Protein Blocks provide an effective approach for protein fold recognition, particularly for challenging twilight zone sequences.
- This method enhances the annotation of protein structures in the twilight zone.
- The Protein Blocks approach offers a valuable tool in structural bioinformatics.
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