High performance set of PseAAC and sequence based descriptors for protein classification

Abstract

The study of reliable automatic systems for protein classification is important for several domains, including finding novel drugs and vaccines. The last decade has seen a number of advances in the development of reliable systems for classifying proteins. Of particular interest has been the exploration of new methods for extracting features from a protein that enhance classification for a given problem. Most methods developed to date, however, have been evaluated in only one or two application areas. Methods have not been explored that generalize well across a number of application areas and datasets. The aim of this study is to find a general method, or an ensemble of methods, that works well on different protein classification datasets and problems. Towards this end, we evaluate several feature extraction approaches for representing proteins starting from their amino acid sequence as well as different feature descriptor combinations using an ensemble of classifiers (support vector machines). In our experiments, more than ten different protein descriptors are compared using nine different datasets. We develop our system using a blind testing protocol, where the parameters of the system are optimized using one dataset and then validated using the other datasets (and so on for each dataset). Although different stand-alone classifiers work well on some datasets and not on others, we have discovered that fusion among different methods obtains a good performance across all the tested datasets, especially when using the weighted sum rule. Included in our feature descriptor combinations is the introduction of two new descriptors, one based on wavelets and the other based on amino acid groups. Using our system, both outperform their standard implementations. We also consider as a baseline the simple amino acid composition (AC) and dipeptide composition (2G), since they have been widely used for protein classification. Our proposed method outperforms AC and 2G.