title: Analysis and Identification of Aptamer-Compound Interactions with a Maximum Relevance Minimum Redundancy and Nearest Neighbor Algorithm.
abstract: The development of biochemistry and molecular biology has revealed an increasingly important role of compounds in several biological processes. Like the aptamer-protein interaction, aptamer-compound interaction attracts increasing attention. However, it is time-consuming to select proper aptamers against compounds using traditional methods, such as exponential enrichment. Thus, there is an urgent need to design effective computational methods for searching effective aptamers against compounds. This study attempted to extract important features for aptamer-compound interactions using feature selection methods, such as Maximum Relevance Minimum Redundancy, as well as incremental feature selection. Each aptamer-compound pair was represented by properties derived from the aptamer and compound, including frequencies of single nucleotides and dinucleotides for the aptamer, as well as the constitutional, electrostatic, quantum-chemical, and space conformational descriptors of the compounds. As a result, some important features were obtained. To confirm the importance of the obtained features, we further discussed the associations between them and aptamer-compound interactions. Simultaneously, an optimal prediction model based on the nearest neighbor algorithm was built to identify aptamer-compound interactions, which has the potential to be a useful tool for the identification of novel aptamer-compound interactions. The program is available upon the request.
authors.affiliation: School of Life Sciences, Shanghai University, Shanghai 200444, China.
authors.forename: ShaoPeng
authors.initials: S
authors.lastname: Wang
authors.affiliation: Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
authors.forename: Yu-Hang
authors.initials: YH
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Molecular Pharmacology and Drug Evaluation (Ministry of Education), Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, School of Pharmacy, Yantai University, Shandong, Yantai 264005, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Lu
authors.affiliation: CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
authors.forename: Weiren
authors.initials: W
authors.lastname: Cui
authors.affiliation: Department of Mathematics and Computer Science, School of Arts and Sciences, University of Houston-Victoria, Victoria, TX 77901, USA.
authors.forename: Jerry
authors.initials: J
authors.lastname: Hu
authors.affiliation: School of Life Sciences, Shanghai University, Shanghai 200444, China.
authors.forename: Yu-Dong
authors.initials: YD
authors.lastname: Cai
mesh_terms: D000465:Algorithms; D052157:Aptamers, Nucleotide / Q000737:chemistry*; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D008962:Models, Theoretical; D008968:Molecular Conformation; D011506:Proteins / Q000737:chemistry*; D011789:Quantum Theory
chemical_list: D052157:Aptamers, Nucleotide; D011506:Proteins