Fine-grained protein fold assignment by support vector machines using generalized npeptide coding schemes and jury voting from multiple-parameter sets.
In the coarse-grained fold assignment of major protein classes, such as all-alpha, all-beta, alpha + beta, alpha/beta proteins, one can easily achieve high prediction accuracy from primary amino acid sequences. However, the fine-grained assignment of folds, such as those defined in the Structural Classification of Proteins (SCOP) database, presents a challenge due to the larger amount of folds available. Recent study yielded reasonable prediction accuracy of 56.0% on an independent set of 27 most populated folds. In this communication, we apply the support vector machine (SVM) method, using a combination of protein descriptors based on the properties derived from the composition of n-peptide and jury voting, to the fine-grained fold prediction, and are able to achieve an overall prediction accuracy of 69.6% on the same independent set-significantly higher than the previous results. On 10-fold cross-validation, we obtained a prediction accuracy of 65.3%. Our results show that SVM coupled with suitable global sequence-coding schemes can significantly improve the fine-grained fold prediction. Our approach should be useful in structure prediction and modeling.
Yu
Chin-Sheng
CS
Department of Biological Science and Technology, National Chiao Tung University, Hsin Chu, Taiwan.
Wang
Jung-Ying
JY
Yang
Jinn-Moon
JM
Lyu
Ping-Chiang
PC
Lin
Chih-Jen
CJ
Hwang
Jenn-Kang
JK
D000818:Animals; D057927:Hydrophobic and Hydrophilic Interactions; D010455:Peptides / Q000737:chemistry; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D020539:Sequence Analysis, Protein / Q000379:methods*
D010455:Peptides; D011506:Proteins