Prediction of protein structural classes for low-homology sequences based on predicted secondary structure
<p>Abstract</p> <p>Background</p> <p>Prediction of protein structural classes (<it>α</it>, <it>β</it>, <it>α </it>+ <it>β </it>and <it>α</it>/<it>β</it>) from amino acid sequences is of great import...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2010-01-01
|
| Series: | BMC Bioinformatics |
| _version_ | 1811266135146889216 |
|---|---|
| author | Chen Xin Peng Zhen-Ling Yang Jian-Yi |
| author_facet | Chen Xin Peng Zhen-Ling Yang Jian-Yi |
| author_sort | Chen Xin |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Prediction of protein structural classes (<it>α</it>, <it>β</it>, <it>α </it>+ <it>β </it>and <it>α</it>/<it>β</it>) from amino acid sequences is of great importance, as it is beneficial to study protein function, regulation and interactions. Many methods have been developed for high-homology protein sequences, and the prediction accuracies can achieve up to 90%. However, for low-homology sequences whose average pairwise sequence identity lies between 20% and 40%, they perform relatively poorly, yielding the prediction accuracy often below 60%.</p> <p>Results</p> <p>We propose a new method to predict protein structural classes on the basis of features extracted from the predicted secondary structures of proteins rather than directly from their amino acid sequences. It first uses PSIPRED to predict the secondary structure for each protein sequence. Then, the <it>chaos game representation </it>is employed to represent the predicted secondary structure as two time series, from which we generate a comprehensive set of 24 features using <it>recurrence quantification analysis</it>, <it>K-string based information entropy </it>and <it>segment-based analysis</it>. The resulting feature vectors are finally fed into a simple yet powerful Fisher's discriminant algorithm for the prediction of protein structural classes. We tested the proposed method on three benchmark datasets in low homology and achieved the overall prediction accuracies of 82.9%, 83.1% and 81.3%, respectively. Comparisons with ten existing methods showed that our method consistently performs better for all the tested datasets and the overall accuracy improvements range from 2.3% to 27.5%. A web server that implements the proposed method is freely available at <url>http://www1.spms.ntu.edu.sg/~chenxin/RKS_PPSC/</url>.</p> <p>Conclusion</p> <p>The high prediction accuracy achieved by our proposed method is attributed to the design of a comprehensive feature set on the predicted secondary structure sequences, which is capable of characterizing the sequence order information, local interactions of the secondary structural elements, and spacial arrangements of <it>α </it>helices and <it>β </it>strands. Thus, it is a valuable method to predict protein structural classes particularly for low-homology amino acid sequences.</p> |
| first_indexed | 2024-04-12T20:37:39Z |
| format | Article |
| id | doaj.art-e36a5884ad66412aaa46aca0d0fc99e5 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-04-12T20:37:39Z |
| publishDate | 2010-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-e36a5884ad66412aaa46aca0d0fc99e52022-12-22T03:17:33ZengBMCBMC Bioinformatics1471-21052010-01-0111Suppl 1S910.1186/1471-2105-11-S1-S9Prediction of protein structural classes for low-homology sequences based on predicted secondary structureChen XinPeng Zhen-LingYang Jian-Yi<p>Abstract</p> <p>Background</p> <p>Prediction of protein structural classes (<it>α</it>, <it>β</it>, <it>α </it>+ <it>β </it>and <it>α</it>/<it>β</it>) from amino acid sequences is of great importance, as it is beneficial to study protein function, regulation and interactions. Many methods have been developed for high-homology protein sequences, and the prediction accuracies can achieve up to 90%. However, for low-homology sequences whose average pairwise sequence identity lies between 20% and 40%, they perform relatively poorly, yielding the prediction accuracy often below 60%.</p> <p>Results</p> <p>We propose a new method to predict protein structural classes on the basis of features extracted from the predicted secondary structures of proteins rather than directly from their amino acid sequences. It first uses PSIPRED to predict the secondary structure for each protein sequence. Then, the <it>chaos game representation </it>is employed to represent the predicted secondary structure as two time series, from which we generate a comprehensive set of 24 features using <it>recurrence quantification analysis</it>, <it>K-string based information entropy </it>and <it>segment-based analysis</it>. The resulting feature vectors are finally fed into a simple yet powerful Fisher's discriminant algorithm for the prediction of protein structural classes. We tested the proposed method on three benchmark datasets in low homology and achieved the overall prediction accuracies of 82.9%, 83.1% and 81.3%, respectively. Comparisons with ten existing methods showed that our method consistently performs better for all the tested datasets and the overall accuracy improvements range from 2.3% to 27.5%. A web server that implements the proposed method is freely available at <url>http://www1.spms.ntu.edu.sg/~chenxin/RKS_PPSC/</url>.</p> <p>Conclusion</p> <p>The high prediction accuracy achieved by our proposed method is attributed to the design of a comprehensive feature set on the predicted secondary structure sequences, which is capable of characterizing the sequence order information, local interactions of the secondary structural elements, and spacial arrangements of <it>α </it>helices and <it>β </it>strands. Thus, it is a valuable method to predict protein structural classes particularly for low-homology amino acid sequences.</p> |
| spellingShingle | Chen Xin Peng Zhen-Ling Yang Jian-Yi Prediction of protein structural classes for low-homology sequences based on predicted secondary structure BMC Bioinformatics |
| title | Prediction of protein structural classes for low-homology sequences based on predicted secondary structure |
| title_full | Prediction of protein structural classes for low-homology sequences based on predicted secondary structure |
| title_fullStr | Prediction of protein structural classes for low-homology sequences based on predicted secondary structure |
| title_full_unstemmed | Prediction of protein structural classes for low-homology sequences based on predicted secondary structure |
| title_short | Prediction of protein structural classes for low-homology sequences based on predicted secondary structure |
| title_sort | prediction of protein structural classes for low homology sequences based on predicted secondary structure |
| work_keys_str_mv | AT chenxin predictionofproteinstructuralclassesforlowhomologysequencesbasedonpredictedsecondarystructure AT pengzhenling predictionofproteinstructuralclassesforlowhomologysequencesbasedonpredictedsecondarystructure AT yangjianyi predictionofproteinstructuralclassesforlowhomologysequencesbasedonpredictedsecondarystructure |