Automated protein classification using consensus decision.
We propose a novel technique for automatically generating the SCOP classification of a protein structure with high accuracy. High accuracy is achieved by combining the decisions of multiple methods using the consensus of a committee (or an ensemble) classifier. Our technique is rooted in machine learning which shows that by judicially employing component classifiers, an ensemble classifier can be constructed to outperform its components. We use two sequence- and three structure-comparison tools as component classifiers. Given a protein structure, using the joint hypothesis, we first determine if the protein belongs to an existing category (family, superfamily, fold) in the SCOP hierarchy. For the proteins that are predicted as members of the existing categories, we compute their family-, superfamily-, and fold-level classifications using the consensus classifier. We show that we can significantly improve the classification accuracy compared to the individual component classifiers. In particular, we achieve error rates that are 3-12 times less than the individual classifiers' error rates at the family level, 1.5-4.5 times less at the superfamily level, and 1.1-2.4 times less at the fold level.
Can
Tolga
T
Department of Computer Science, University of California at Santa Barbara, 93106, USA. tcan@cs.ucsb.edu
Camoğlu
Orhan
O
Singh
Ambuj K
AK
Wang
Yuan-Fang
YF
D000465:Algorithms; D000595:Amino Acid Sequence; D001185:Artificial Intelligence; D016000:Cluster Analysis; D016384:Consensus Sequence; D003661:Decision Support Techniques; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated / Q000379:methods*; D011506:Proteins / Q000032:analysis / Q000737:chemistry* / Q000145:classification*; D020539:Sequence Analysis, Protein / Q000379:methods*
D011506:Proteins