BMC Bioinformatics, 11(Suppl 1), S9p. (2010) DOI:10.1186/1471-2105-11-S1-S9

Prediction of protein structural classes for low-homology sequences based on predicted secondary structure

J. Yang, Z. Peng, X. Chen

Background
Prediction of protein structural classes (α, β, α+ β and α/β) 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%.

Results
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 chaos game representation is employed to represent the predicted secondary structure as two time series, from which we generate a comprehensive set of 24 features using recurrence quantification analysis, K-string based information entropy and segment-based analysis. 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 http://www1.spms.ntu.edu.sg/ chenxin/RKS_PPSC/ webcite.

Conclusion
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 αhelices and β strands. Thus, it is a valuable method to predict protein structural classes particularly for low-homology amino acid sequences.

back


Creative Commons License © 2017 SOME RIGHTS RESERVED
The content of this web site is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 2.0 Germany License.

Please note: The abstracts of the bibliography database may underly other copyrights.

Ihr Browser versucht gerade eine Seite aus dem sogenannten Internet auszudrucken. Das Internet ist ein weltweites Netzwerk von Computern, das den Menschen ganz neue Möglichkeiten der Kommunikation bietet.

Da Politiker im Regelfall von neuen Dingen nichts verstehen, halten wir es für notwendig, sie davor zu schützen. Dies ist im beidseitigen Interesse, da unnötige Angstzustände bei Ihnen verhindert werden, ebenso wie es uns vor profilierungs- und machtsüchtigen Politikern schützt.

Sollten Sie der Meinung sein, dass Sie diese Internetseite dennoch sehen sollten, so können Sie jederzeit durch normalen Gebrauch eines Internetbrowsers darauf zugreifen. Dazu sind aber minimale Computerkenntnisse erforderlich. Sollten Sie diese nicht haben, vergessen Sie einfach dieses Internet und lassen uns in Ruhe.

Die Umgehung dieser Ausdrucksperre ist nach §95a UrhG verboten.

Mehr Informationen unter www.politiker-stopp.de.