Predicting Protein Functional Class with the Weighted Segmented Pseudo-Amino Acid Composition Moment Vector
نویسندگان
چکیده
Predicting protein function at the proteomic-scale is one of the fundamental goals in cell biology and proteomics. In this paper, we proposed a new method for characterizing protein sequences—the Weighted Segmented Pseudo-amino acid composition Moment Vector (W-SPsAA-MV). From protein sequences, the encoding method of W-SPsAA-MV is applied to protein functional class prediction associated with the nearest neighbor algorithm (NNA) and covariant discriminant (CD) classifier. The experiment results show that our new method is efficient to predict functional class of query proteins when protein-protein interaction information is limited. ` Corresponding author. E-mail address: [email protected] (X.Y. Zhou) MATCH Communications in Mathematical and in Computer Chemistry MATCH Commun. Math. Comput. Chem. 66 (2011) 445-462
منابع مشابه
Using grey dynamic modeling and pseudo amino acid composition to predict protein structural classes
Using the pseudo amino acid (PseAA) composition to represent the sample of a protein can incorporate a considerable amount of sequence pattern information so as to improve the prediction quality for its structural or functional classification. However, how to optimally formulate the PseAA composition is an important problem yet to be solved. In this article the grey modeling approach is introdu...
متن کاملWeighted-support vector machines for predicting membrane protein types based on pseudo-amino acid composition.
Membrane proteins are generally classified into the following five types: (1) type I membrane proteins, (2) type II membrane proteins, (3) multipass transmembrane proteins, (4) lipid chain-anchored membrane proteins and (5) GPI-anchored membrane proteins. Prediction of membrane protein types has become one of the growing hot topics in bioinformatics. Currently, we are facing two critical challe...
متن کاملComparison the functional properties of protein Hydrolysates from poultry byproducts and rainbow trout
Poultry by-products and rainbow trout (Onchorhynchus mykiss) viscera are abundant and underutilized resources that can be used as a unique protein source to make protein hydrolysates. In this study protein hydrolysate were made from these two different sources with Alcalase 2.4L. The functional properties of Fish viscera protein hydrolysate (FPH) compared to poultry by-products protein hydrolys...
متن کاملPrediction of enzyme subfamily class via pseudo amino acid composition by incorporating the conjoint triad feature.
Predicting enzyme subfamily class is an imbalance multi-class classification problem due to the fact that the number of proteins in each subfamily makes a great difference. In this paper, we focus on developing the computational methods specially designed for the imbalance multi-class classification problem to predict enzyme subfamily class. We compare two support vector machine (SVM)-based met...
متن کاملPrediction of protein structure classes with pseudo amino acid composition and fuzzy support vector machine network.
It is a critical challenge to develop automated methods for fast and accurately determining the structures of proteins because of the increasingly widening gap between the number of sequence-known proteins and that of structure-known proteins in the post-genomic age. The knowledge of protein structural class can provide useful information towards the determination of protein structure. Thus, it...
متن کامل