title: Identification of protein-interacting nucleotides in a RNA sequence using composition profile of tri-nucleotides.
abstract: The RNA-protein interactions play a diverse role in the cells, thus identification of RNA-protein interface is essential for the biologist to understand their function. In the past, several methods have been developed for predicting RNA interacting residues in proteins, but limited efforts have been made for the identification of protein-interacting nucleotides in RNAs. In order to discriminate protein-interacting and non-interacting nucleotides, we used various classifiers (NaiveBayes, NaiveBayesMultinomial, BayesNet, ComplementNaiveBayes, MultilayerPerceptron, J48, SMO, RandomForest, SMO and SVM(light)) for prediction model development using various features and achieved highest 83.92% sensitivity, 84.82 specificity, 84.62% accuracy and 0.62 Matthew's correlation coefficient by SVM(light) based models. We observed that certain tri-nucleotides like ACA, ACC, AGA, CAC, CCA, GAG, UGA, and UUU preferred in protein-interaction. All the models have been developed using a non-redundant dataset and are evaluated using five-fold cross validation technique. A web-server called RNApin has been developed for the scientific community (http://crdd.osdd.net/raghava/rnapin/).
authors: Bioinformatics Centre, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, India. Electronic address: bharat@imtech.res.in.
authors: Bharat
authors: B
authors: Panwar
authors: Bioinformatics Centre, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, India. Electronic address: http://www.imtech.res.in/raghava/
authors: Gajendra P S
authors: GP
authors: Raghava
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D008958:Models, Molecular; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D060388:Support Vector Machine
chemical_list: D016601:RNA-Binding Proteins; D012313:RNA
keywords: Binary profile of patterns (BPP); Prediction; Protein-interacting nucleotide (PIN); RNApin; SVM; Tri-nucleotide composition profile of patterns (TNCPP)