title: A knowledge-based orientation potential for transcription factor-DNA docking.
abstract: BACKGROUND
  Computational modeling of protein-DNA complexes remains a challenging problem in structural bioinformatics. One of the key factors for a successful protein-DNA docking is a potential function that can accurately discriminate the near-native structures from decoy complexes and at the same time make conformational sampling more efficient. Here, we developed a novel orientation-dependent, knowledge-based, residue-level potential for improving transcription factor (TF)-DNA docking.
  
  
  RESULTS
  We demonstrated the performance of this new potential in TF-DNA binding affinity prediction, discrimination of native protein-DNA complex from decoy structures, and most importantly in rigid TF-DNA docking. The rigid TF-DNA docking with the new orientation potential, on a benchmark of 38 complexes, successfully predicts 42% of the cases with root mean square deviations lower than 1 Å and 55% of the cases with root mean square deviations lower than 3 Å. The results suggest that docking with this new orientation-dependent, coarse-grained statistical potential can achieve high-docking accuracy and can serve as a crucial first step in multi-stage flexible protein-DNA docking.
  
  
  METHODS
  The new potential is available at http://bioinfozen.uncc.edu/Protein_DNA_orientation_potential.tar.
authors.affiliation: Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
authors.forename: Takako
authors.initials: T
authors.lastname: Takeda
authors.forename: Rosario I
authors.initials: RI
authors.lastname: Corona
authors.forename: Jun-Tao
authors.initials: JT
authors.lastname: Guo
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D051188:Knowledge Bases; D062105:Molecular Docking Simulation / Q000379:methods*; D011485:Protein Binding; D014157:Transcription Factors / Q000737:chemistry* / Q000378:metabolism
chemical_list: D014157:Transcription Factors; D004247:DNA