Prediction of protein secondary structures with a novel kernel density estimation based classifier.

BMC Research Notes
Darby Tien-Hao ChangYen-Jen Oyang

Abstract

Though prediction of protein secondary structures has been an active research issue in bioinformatics for quite a few years and many approaches have been proposed, a new challenge emerges as the sizes of contemporary protein structure databases continue to grow rapidly. The new challenge concerns how we can effectively exploit all the information implicitly deposited in the protein structure databases and deliver ever-improving prediction accuracy as the databases expand rapidly. The new challenge is addressed in this article by proposing a predictor designed with a novel kernel density estimation algorithm. One main distinctive feature of the kernel density estimation based approach is that the average execution time taken by the training process is in the order of O(nlogn), where n is the number of instances in the training dataset. In the experiments reported in this article, the proposed predictor delivered an average Q3 (three-state prediction accuracy) score of 80.3% and an average SOV (segment overlap) score of 76.9% for a set of 27 benchmark protein chains extracted from the EVA server that are longer than 100 residues. The experimental results reported in this article reveal that we can continue to achieve higher predi...Continue Reading

References

Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Jun 27, 2000·Bioinformatics·L J McGuffinD T Jones
Jan 25, 2002·Proteins·Dariusz Przybylski, Burkhard Rost
Sep 12, 2003·Bioinformatics·J J WardD T Jones
Mar 1, 2005·IEEE Transactions on Neural Networks·Yen-Jen OyangZhi-Wei Chen
Jun 16, 2006·BMC Bioinformatics·Scott MontgomerieDavid S Wishart
Feb 5, 2008·IEEE Transactions on Neural Networks·Chih-Wei Hsu, Chih-Jen Lin

❮ Previous
Next ❯

Citations

Mar 10, 2010·Journal of Chemical Information and Modeling·Joji M OtakiHaruhiko Yamamoto

❮ Previous
Next ❯

Software Mentioned

EVA
Prote2S
PSIPRED
LIBSVM
PSI
DSSP
BLAST

Related Concepts

Related Feeds

Cajal Bodies & Gems

Cajal bodies or coiled bodies are dense foci of coilin protein. Gemini of Cajal bodies, or gems, are microscopically similar to Cajal bodies. It is believed that Cajal bodies play important roles in RNA processing while gems assist the Cajal bodies. Find the latest research on Cajal bodies and gems here.

Related Papers

Proceedings of the National Academy of Sciences of the United States of America
Michael P H StumpfCarsten Wiuf
Nucleic Acids Research
Gopa R MishraAkhilesh Pandey
© 2022 Meta ULC. All rights reserved