title: Identification of DNA-binding proteins using multi-features fusion and binary firefly optimization algorithm.
abstract: BACKGROUND
  DNA-binding proteins (DBPs) play fundamental roles in many biological processes. Therefore, the developing of effective computational tools for identifying DBPs is becoming highly desirable.
  
  
  RESULTS
  In this study, we proposed an accurate method for the prediction of DBPs. Firstly, we focused on the challenge of improving DBP prediction accuracy with information solely from the sequence. Secondly, we used multiple informative features to encode the protein. These features included evolutionary conservation profile, secondary structure motifs, and physicochemical properties. Thirdly, we introduced a novel improved Binary Firefly Algorithm (BFA) to remove redundant or noisy features as well as select optimal parameters for the classifier. The experimental results of our predictor on two benchmark datasets outperformed many state-of-the-art predictors, which revealed the effectiveness of our method. The promising prediction performance on a new-compiled independent testing dataset from PDB and a large-scale dataset from UniProt proved the good generalization ability of our method. In addition, the BFA forged in this research would be of great potential in practical applications in optimization fields, especially in feature selection problems.
  
  
  CONCLUSIONS
  A highly accurate method was proposed for the identification of DBPs. A user-friendly web-server named iDbP (identification of DNA-binding Proteins) was constructed and provided for academic use.
authors: School of Computer Science and Information Technology, Northeast Normal University, Changchun, 130117, People's Republic of China.
authors: Jian
authors: J
authors: Zhang
authors: School of Computer Science and Information Technology, Northeast Normal University, Changchun, 130117, People's Republic of China.
authors: Bo
authors: B
authors: Gao
authors: School of Computer Science and Information Technology, Northeast Normal University, Changchun, 130117, People's Republic of China.
authors: Haiting
authors: H
authors: Chai
authors: School of Computer Science and Information Technology, Northeast Normal University, Changchun, 130117, People's Republic of China.
authors: Zhiqiang
authors: Z
authors: Ma
authors: School of Computer Science and Information Technology, Northeast Normal University, Changchun, 130117, People's Republic of China. guifuyang.nenu@gmail.com.|Office of Informatization Management and Planning, Northeast Normal University, Changchun, 130117, People's Republic of China. guifuyang.nenu@gmail.com.
authors: Guifu
authors: G
authors: Yang
mesh_terms: D000465:Algorithms; D019540:Area Under Curve; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism*; D030562:Databases, Protein; D020407:Internet; D017433:Protein Structure, Secondary; D012372:ROC Curve; D014584:User-Computer Interface
chemical_list: D004268:DNA-Binding Proteins
keywords: Binary firefly algorithm; DNA-binding proteins; Feature selection; Parameters optimization