title: Shape string: a new feature for prediction of DNA-binding residues.
abstract: Protein-DNA interactions are involved in many biological processes essential for gene expression and regulation. To understand the molecular mechanisms of protein-DNA recognition, it is crucial to analyze and identify DNA-binding residues of protein-DNA complexes. Here, we proposed a novel descriptor shape string and another two related features shape string PSSM and shape string pair composition to characterize DNA-binding residues. We employed the new features and the position-specific scoring matrix (PSSM) for modeling and prediction. The results of a benchmark dataset showed that our approach significantly improved the accuracy of the predictor. The overall accuracy of our approach reached 85.86% with 85.02% sensitivity and 86.02% specificity. The results also demonstrated that shape string is a powerful descriptor for the prediction of DNA-binding residues. The additional two related features enhanced the predictive value.
authors.affiliation: Department of Chemistry, Tongji University, Shanghai 200092, PR China.
authors.forename: Duo-Duo
authors.initials: DD
authors.lastname: Wang
authors.forename: Tong-Hua
authors.initials: TH
authors.lastname: Li
authors.forename: Jiang-Ming
authors.initials: JM
authors.lastname: Sun
authors.forename: Da-Peng
authors.initials: DP
authors.lastname: Li
authors.forename: Wen-Wei
authors.initials: WW
authors.lastname: Xiong
authors.forename: Wen-Yan
authors.initials: WY
authors.lastname: Wang
authors.forename: Sheng-Nan
authors.initials: SN
authors.lastname: Tang
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001665:Binding Sites; D004247:DNA / Q000737:chemistry*; D030562:Databases, Protein; D008958:Models, Molecular; D008969:Molecular Sequence Data; D056510:Position-Specific Scoring Matrices; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D011506:Proteins / Q000737:chemistry*; D012680:Sensitivity and Specificity; D012984:Software
chemical_list: D011506:Proteins; D004247:DNA