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Template-based quaternary structure prediction of proteins using enhanced profile-profile alignments
Tsukasa Nakamura1,2, Toshiyuki Oda1, Yoshinori Fukasawa1
1Artificial Intelligence Research Center (AIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.
Proteins
|November 28, 2017
Summary
Predicting protein complex structures is crucial for understanding protein function. Template-Based Modeling (TBM) using enhanced profile-profile alignments proved effective in identifying templates for quaternary structure prediction.
Area of Science:
- Structural biology
- Computational biology
- Biophysics
Background:
- Proteins function as biological assemblies, requiring elucidation of their quaternary structure for functional understanding.
- Template-Based Modeling (TBM) is a widely used approach for protein structure prediction, increasingly valuable with growing structural and sequence data.
- Predicting biological assembly structures is challenging but essential, with increasing protein complex data available.
Purpose of the Study:
- To present the methodology and retrospective analysis of the FONT team's approach for the Quaternary Structure Prediction category at CASP12.
- To evaluate the effectiveness of enhanced profile-profile alignments in identifying suitable templates for biological assembly structure prediction.
- To assess the utility of template identification for medium and hard quaternary structure prediction cases.
Main Methods:
- Utilized enhanced profile-profile alignments based on the FORTE algorithm for template identification.
- Participated in the 12th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP12) under Group #480 (FONT team).
- Performed retrospective analyses of experimental procedures and results for quaternary structure prediction.
Main Results:
- Enhanced profile-profile alignments successfully identified templates in nearly all tested cases.
- The study highlighted the necessity for developing improved model selection methods to enhance prediction accuracy.
- Finding templates for protein complexes was found to be beneficial even for medium and hard assembly prediction challenges.
Conclusions:
- Enhanced profile-profile alignment is a robust method for identifying templates in quaternary structure prediction.
- Further development of model selection strategies is crucial for improving the accuracy of biological assembly predictions.
- Template-based approaches remain valuable for predicting complex protein structures, including challenging cases.
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