title: An all-atom knowledge-based energy function for protein-DNA threading, docking decoy discrimination, and prediction of transcription-factor binding profiles.
abstract: How to make an accurate representation of protein-DNA interaction by an energy function is a long-standing unsolved problem in structural biology. Here, we modified a statistical potential based on the distance-scaled, finite ideal-gas reference state so that it is optimized for protein-DNA interactions. The changes include a volume-fraction correction to account for unmixable atom types in proteins and DNA in addition to the usage of a low-count correction, residue/base-specific atom types, and a shorter cutoff distance for protein-DNA interactions. The new statistical energy functions are tested in threading and docking decoy discriminations and prediction of protein-DNA binding affinities and transcription-factor binding profiles. The results indicate that new proposed energy functions are among the best in existing energy functions for protein-DNA interactions. The new energy functions are available as a web-server called DDNA 2.0 at http://sparks.informatics.iupui.edu. The server version was trained by the entire 212 protein-DNA complexes.
authors.affiliation: Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui, China.
authors.forename: Beisi
authors.initials: B
authors.lastname: Xu
authors.forename: Yuedong
authors.initials: Y
authors.lastname: Yang
authors.forename: Haojun
authors.initials: H
authors.lastname: Liang
authors.forename: Yaoqi
authors.initials: Y
authors.lastname: Zhou
mesh_terms: D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D013816:Thermodynamics; D014157:Transcription Factors / Q000737:chemistry* / Q000378:metabolism
chemical_list: D014157:Transcription Factors; D004247:DNA