A mixture of physicochemical and evolutionary-based feature extraction approaches for protein fold recognition

• Published in: International journal of data mining and bioinformatics Vol. 11; no. 1; p. 115
• Main Authors: Dehzangi, Abdollah, Sharma, Alok, Lyons, James, Paliwal, Kuldip K, Sattar, Abdul
• Format: Journal Article
• Language: English
• Published: Switzerland 01.01.2015
• Subjects: Amino Acid Sequence; Base Sequence; Computer Simulation; Evolution, Molecular; Models, Chemical; Models, Genetic; Models, Molecular; Molecular Sequence Data; Pattern Recognition, Automated - methods; Protein Folding; Protein Structure, Tertiary; Proteins - chemistry; Proteins - ultrastructure; Sequence Analysis - methods
• ISSN: 1748-5673; 1748-5681
• DOI: 10.1504/IJDMB.2015.066359

Recent advancement in the pattern recognition field stimulates enormous interest in Protein Fold Recognition (PFR). PFR is considered as a crucial step towards protein structure prediction and drug design. Despite all the recent achievements, the PFR still remains as an unsolved issue in biological science and its prediction accuracy still remains unsatisfactory. Furthermore, the impact of using a wide range of physicochemical-based attributes on the PFR has not been adequately explored. In this study, we propose a novel mixture of physicochemical and evolutionary-based feature extraction methods based on the concepts of segmented distribution and density. We also explore the impact of 55 different physicochemical-based attributes on the PFR. Our results show that by providing more local discriminatory information as well as obtaining benefit from both physicochemical and evolutionary-based features simultaneously, we can enhance the protein fold prediction accuracy up to 5% better than previously reported results found in the literature.