title: PreDNA: accurate prediction of DNA-binding sites in proteins by integrating sequence and geometric structure information.
abstract: BACKGROUND
  Protein-DNA interactions often take part in various crucial processes, which are essential for cellular function. The identification of DNA-binding sites in proteins is important for understanding the molecular mechanisms of protein-DNA interaction. Thus, we have developed an improved method to predict DNA-binding sites by integrating structural alignment algorithm and support vector machine-based methods.
  
  
  RESULTS
  Evaluated on a new non-redundant protein set with 224 chains, the method has 80.7% sensitivity and 82.9% specificity in the 5-fold cross-validation test. In addition, it predicts DNA-binding sites with 85.1% sensitivity and 85.3% specificity when tested on a dataset with 62 protein-DNA complexes. Compared with a recently published method, BindN+, our method predicts DNA-binding sites with a 7% better area under the receiver operating characteristic curve value when tested on the same dataset. Many important problems in cell biology require the dense non-linear interactions between functional modules be considered. Thus, our prediction method will be useful in detecting such complex interactions.
authors: Laboratory of Theoretical Biophysics, School of Physical Sciences and Technology, College of Computer Science and The National Research Center for Animal Transgenic Biotechnology, Inner Mongolia University, Hohhot, 010021, China.
authors: Tao
authors: T
authors: Li
authors: Qian-Zhong
authors: QZ
authors: Li
authors: Shuai
authors: S
authors: Liu
authors: Guo-Liang
authors: GL
authors: Fan
authors: Yong-Chun
authors: YC
authors: Zuo
authors: Yong
authors: Y
authors: Peng
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D017433:Protein Structure, Secondary; D012372:ROC Curve; D020539:Sequence Analysis, Protein; D060388:Support Vector Machine
chemical_list: D004268:DNA-Binding Proteins; D004247:DNA