Evaluation of protein dihedral angle prediction methods

Tertiary structure prediction of a protein from its amino acid sequence is one of the major challenges in the field of bioinformatics. Hierarchical approach is one of the persuasive techniques used for predicting protein tertiary structure, especially in the absence of homologous protein structures....

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Bibliographic Details
Published in:PloS one 2014-08, Vol.9 (8), p.e105667-e105667
Main Authors: Singh, Harinder, Singh, Sandeep, Raghava, Gajendra P S
Format: Article
Language:English
Subjects:
Algorithms
Amino acid sequence
Analysis
Bioinformatics
Biology and Life Sciences
Computational Biology
Databases, Protein
Datasets
Dihedral angle
Evaluation
Glycine
Homology
Methods
Neural networks
Predictions
Proline
Protein folding
Protein structure
Protein Structure, Tertiary
Proteins
Proteins - chemistry
Secondary structure
Spine
Structural hierarchy
Tertiary structure
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Summary:Tertiary structure prediction of a protein from its amino acid sequence is one of the major challenges in the field of bioinformatics. Hierarchical approach is one of the persuasive techniques used for predicting protein tertiary structure, especially in the absence of homologous protein structures. In hierarchical approach, intermediate states are predicted like secondary structure, dihedral angles, Cα-Cα distance bounds, etc. These intermediate states are used to restraint the protein backbone and assist its correct folding. In the recent years, several methods have been developed for predicting dihedral angles of a protein, but it is difficult to conclude which method is better than others. In this study, we benchmarked the performance of dihedral prediction methods ANGLOR and SPINE X on various datasets, including independent datasets. TANGLE dihedral prediction method was not benchmarked (due to unavailability of its standalone) and was compared with SPINE X and ANGLOR on only ANGLOR dataset on which TANGLE has reported its results. It was observed that SPINE X performed better than ANGLOR and TANGLE, especially in case of prediction of dihedral angles of glycine and proline residues. The analysis suggested that angle shifting was the foremost reason of better performance of SPINE X. We further evaluated the performance of the methods on independent ccPDB30 dataset and observed that SPINE X performed better than ANGLOR.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0105667