title: RAFP-Pred: Robust Prediction of Antifreeze Proteins Using Localized Analysis of n-Peptide Compositions.
abstract: In extreme cold weather, living organisms produce Antifreeze Proteins (AFPs) to counter the otherwise lethal intracellular formation of ice. Structures and sequences of various AFPs exhibit a high degree of heterogeneity, consequently the prediction of the AFPs is considered to be a challenging task. In this research, we propose to handle this arduous manifold learning task using the notion of localized processing. In particular, an AFP sequence is segmented into two sub-segments each of which is analyzed for amino acid and di-peptide compositions. We propose to use only the most significant features using the concept of information gain (IG) followed by a random forest classification approach. The proposed RAFP-Pred achieved an excellent performance on a number of standard datasets. We report a high Youden's index (sensitivity+specificity-1) value of 0.75 on the standard independent test data set outperforming the AFP-PseAAC, AFP_PSSM, AFP-Pred, and iAFP by a margin of 0.05, 0.06, 0.14, and 0.68, respectively. The verification rate on the UniProKB dataset is found to be 83.19 percent which is substantially superior to the 57.18 percent reported for the iAFP method.
authors.forename: Shujaat
authors.initials: S
authors.lastname: Khan
authors.forename: Imran
authors.initials: I
authors.lastname: Naseem
authors.forename: Roberto
authors.initials: R
authors.lastname: Togneri
authors.forename: Mohammed
authors.initials: M
authors.lastname: Bennamoun
mesh_terms: D000465:Algorithms; D021301:Antifreeze Proteins / Q000032:analysis / Q000737:chemistry* / Q000145:classification; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D004151:Dipeptides / Q000032:analysis / Q000737:chemistry*; D000069550:Machine Learning; D012372:ROC Curve; D020539:Sequence Analysis, Protein / Q000379:methods*
chemical_list: D021301:Antifreeze Proteins; D004151:Dipeptides