title: Structural classification of proteins using texture descriptors extracted from the cellular automata image.
abstract: Nowadays, having knowledge about cellular attributes of proteins has an important role in pharmacy, medical science and molecular biology. These attributes are closely correlated with the function and three-dimensional structure of proteins. Knowledge of protein structural class is used by various methods for better understanding the protein functionality and folding patterns. Computational methods and intelligence systems can have an important role in performing structural classification of proteins. Most of protein sequences are saved in databanks as characters and strings and a numerical representation is essential for applying machine learning methods. In this work, a binary representation of protein sequences is introduced based on reduced amino acids alphabets according to surrounding hydrophobicity index. Many important features which are hidden in these long binary sequences can be clearly displayed through their cellular automata images. The extracted features from these images are used to build a classification model by support vector machine. Comparing to previous studies on the several benchmark datasets, the promising classification rates obtained by tenfold cross-validation imply that the current approach can help in revealing some inherent features deeply hidden in protein sequences and improve the quality of predicting protein structural class.
authors: Department of Computer Science and Information Technology, Institute for Advanced Studies in Basic Sciences (IASBS), 45137-66731, Zanjan, Iran.
authors: Hamidreza
authors: H
authors: Kavianpour
authors: Department of Computer Science and Information Technology, Institute for Advanced Studies in Basic Sciences (IASBS), 45137-66731, Zanjan, Iran. vasighi@iasbs.ac.ir.
authors: Mahdi
authors: http://orcid.org/0000-0002-3048-4638
authors: M
authors: Vasighi
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry*; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D057927:Hydrophobic and Hydrophilic Interactions; D011506:Proteins / Q000737:chemistry* / Q000145:classification* / Q000378:metabolism
chemical_list: D000596:Amino Acids; D011506:Proteins
keywords: Amino acid digital coding; Cellular automata; Protein sequence classification; Texture features