A novel machine learning method for cytokine-receptor interaction prediction

Comb Chem High Throughput Screen. 2016;19(2):144-52. doi: 10.2174/1386207319666151110122621.

Abstract

Most essential functions are associated with various protein-protein interactions, particularly the cytokine-receptor interaction. Knowledge of the heterogeneous network of cytokine- receptor interactions provides insights into various human physiological functions. However, only a few studies are focused on the computational prediction of these interactions. In this study, we propose a novel machine-learning-based method for predicting cytokine-receptor interactions. A protein sequence is first transformed by incorporating the sequence evolutional information and then formulated with the following three aspects: (1) the k-skip-n-gram model, (2) physicochemical properties, and (3) local pseudo position-specific score matrix (local PsePSSM). The random forest classifier is subsequently employed to predict potential cytokine-receptor interactions. Experimental results on a dataset of Homo sapiens show that the proposed method exhibits improved performance, with 3.4% higher overall prediction accuracy, than existing methods.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cytokines / chemistry*
  • Cytokines / metabolism
  • Databases, Protein
  • High-Throughput Screening Assays
  • Humans
  • Machine Learning*
  • Protein Binding
  • Receptors, Cytokine / chemistry*
  • Receptors, Cytokine / metabolism

Substances

  • Cytokines
  • Receptors, Cytokine